I just booted with a newly custom compiled/installed 2.6.16 on my
debian/testing. the first suspicious lines in my /var/log/boot show
towards the end of the quoted section below;

****************************************************************
Mon Sep 18 12:03:45 2006: .
Mon Sep 18 12:03:45 2006: Setting parameters of disc: (none).
Mon Sep 18 12:03:45 2006: Will now activate swap.
Mon Sep 18 12:03:45 2006: swapon on /dev/hdb7
Mon Sep 18 12:03:45 2006: Done activating swap.
Mon Sep 18 12:03:45 2006: Will now check root file system.
Mon Sep 18 12:03:45 2006: fsck 1.39 (29-May-2006)
Mon Sep 18 12:03:45 2006: [/sbin/fsck.ext3 (1) -- /] fsck.ext3 -a -C0 /dev/hdb1
Mon Sep 18 12:03:45 2006: /: clean, 10146/136544 files, 104083/273073 blocks
Mon Sep 18 12:03:45 2006: Done checking root file system.
Mon Sep 18 12:03:45 2006: A log will be saved in /var/log/fsck/checkroot if that location is writable.
Mon Sep 18 12:03:45 2006: Setting the system clock..
Mon Sep 18 12:03:45 2006: System Clock set. Local time: Mon Sep 18 12:03:44 EST 2006.
Mon Sep 18 12:03:45 2006: Cleaning up ifupdown...done.
Mon Sep 18 12:03:45 2006: Loading modules...
Mon Sep 18 12:03:45 2006: ide-cd
Mon Sep 18 12:03:45 2006: FATAL: Module ide_cd not found.
Mon Sep 18 12:03:45 2006: ide-detect
Mon Sep 18 12:03:45 2006: FATAL: Module ide_detect not found.
Mon Sep 18 12:03:45 2006: ide-disk
Mon Sep 18 12:03:45 2006: FATAL: Module ide_disk not found.
Mon Sep 18 12:03:45 2006: psmouse
Mon Sep 18 12:03:45 2006: FATAL: Module psmouse not found.
Mon Sep 18 12:03:45 2006: All modules loaded.
Mon Sep 18 12:03:45 2006: Setting the system clock again..
****************************************************************

see all those FATAL:... lines.

is this something I need to worry about?

thanks

How well do your mouse, filesystem and cdrom drive(s) work?

Well, either you compiled into your kernel your mouse and cdrom driver, or else they aren't there. The terminology for psmouse and ide-disk is not proper in the newer kernels. Looks like you have a remnant from some old config in there. psaux is proper. psmouse I haven't seen in 7 years.

I am able to mount and read both cdrow and dvd, mouse works fine, I am logged in the Internet and seams like no problems.
and just for ref. the rest of the /var/log/boot is below

******************************************************************************8
Mon Sep 18 12:41:39 2006: Loading device-mapper support.
Mon Sep 18 12:41:39 2006: Will now check all file systems.
Mon Sep 18 12:41:39 2006: fsck 1.39 (29-May-2006)
Mon Sep 18 12:41:39 2006: Checking all file systems.
Mon Sep 18 12:41:39 2006: [/sbin/fsck.ext3 (1) -- /home] fsck.ext3 -a -C0 /dev/hdb9
Mon Sep 18 12:41:39 2006: /home: clean, 6726/1267968 files, 120826/2534245 blocks (check in 5 mounts)
Mon Sep 18 12:41:39 2006: [/sbin/fsck.ext3 (1) -- /tmp] fsck.ext3 -a -C0 /dev/hdb8
Mon Sep 18 12:41:39 2006: /tmp: clean, 17/192768 files, 32462/393217 blocks (check in 5 mounts)
Mon Sep 18 12:41:39 2006: [/sbin/fsck.ext3 (1) -- /usr] fsck.ext3 -a -C0 /dev/hdb5
Mon Sep 18 12:41:39 2006: /usr: clean, 103494/610432 files, 422739/1220932 blocks (check in 5 mounts)
Mon Sep 18 12:41:39 2006: [/sbin/fsck.ext3 (1) -- /var] fsck.ext3 -a -C0 /dev/hdb6
Mon Sep 18 12:41:39 2006: /var: clean, 5122/366528 files, 315080/732957 blocks (check in 5 mounts)
Mon Sep 18 12:41:39 2006: Done checking file systems.
Mon Sep 18 12:41:39 2006: A log is being saved in /var/log/fsck/checkfs if that location is writable.
Mon Sep 18 12:41:39 2006: Start setting kernel variables via /proc...
Mon Sep 18 12:41:39 2006: Done setting kernel variables via /proc.
Mon Sep 18 12:41:39 2006: Will now mount local filesystems.
Mon Sep 18 12:41:39 2006: /dev/hdb9 on /home type ext3 (rw)
Mon Sep 18 12:41:39 2006: /dev/hdb8 on /tmp type ext3 (rw)
Mon Sep 18 12:41:39 2006: /dev/hdb5 on /usr type ext3 (rw)
Mon Sep 18 12:41:39 2006: /dev/hdb6 on /var type ext3 (rw)
Mon Sep 18 12:41:39 2006: Done mounting local filesystems.
Mon Sep 18 12:41:39 2006: Will now activate swapfile swap.
Mon Sep 18 12:41:39 2006: Done activating swapfile swap.
Mon Sep 18 12:41:39 2006: Detecting hardware...Discovered hardware for these modules: agpgart 3c59x natsemi piix emu10k1 usb_uhci
Mon Sep 18 12:41:40 2006: ^[[33m*^[[39;49m Skipping unavailable/built-in agpgart module.
Mon Sep 18 12:41:40 2006: ^[[33m*^[[39;49m Skipping already loaded module 3c59x.
Mon Sep 18 12:41:41 2006: ^[[33m*^[[39;49m Skipping unavailable/built-in natsemi module.
Mon Sep 18 12:41:41 2006: ^[[33m*^[[39;49m Skipping unavailable/built-in piix module.
Mon Sep 18 12:41:41 2006: ^[[33m*^[[39;49m Skipping unavailable/built-in emu10k1 module.
Mon Sep 18 12:41:41 2006: ^[[33m*^[[39;49m Skipping already loaded module uhci_hcd.
Mon Sep 18 12:41:41 2006: Cleaning /tmp...done.
Mon Sep 18 12:41:41 2006: Cleaning /var/run...done.
Mon Sep 18 12:41:41 2006: Cleaning /var/lock...done.
Mon Sep 18 12:41:42 2006: Setting up resolvconf.../etc/resolvconf/update.d/libc: Warning: /etc/resolv.conf is not a symbolic link to /etc/resolvconf/run/resolv.conf
Mon Sep 18 12:41:42 2006: done.
Mon Sep 18 12:41:42 2006: Running 0dns-down to make sure resolv.conf is ok...done.
Mon Sep 18 12:41:42 2006: Setting up networking...done.
Mon Sep 18 12:41:42 2006: Setting hostname to 'debian'...done.
Mon Sep 18 12:41:42 2006: ^[[33m*^[[39;49m /etc/network/options is deprecated.
Mon Sep 18 12:41:42 2006: Setting up IP spoofing protection...done (rp_filter).
Mon Sep 18 12:41:42 2006: Configuring network interfaces...Internet Software Consortium DHCP Client 2.0pl5
Mon Sep 18 12:41:43 2006: Copyright 1995, 1996, 1997, 1998, 1999 The Internet Software Consortium.
Mon Sep 18 12:41:43 2006: All rights reserved.
Mon Sep 18 12:41:43 2006:
Mon Sep 18 12:41:43 2006: Please contribute if you find this software useful.
Mon Sep 18 12:41:43 2006: For info, please visit http://www.isc.org/dhcp-contrib.html
Mon Sep 18 12:41:43 2006:
Mon Sep 18 12:41:44 2006: Listening on LPF/eth0/00:10:5a:6d:b3:3d
Mon Sep 18 12:41:44 2006: Sending on LPF/eth0/00:10:5a:6d:b3:3d
Mon Sep 18 12:41:44 2006: Sending on Socket/fallback/fallback-net
Mon Sep 18 12:41:44 2006: DHCPDISCOVER on eth0 to 255.255.255.255 port 67 interval 3
Mon Sep 18 12:41:44 2006: DHCPOFFER from 192.168.1.1
Mon Sep 18 12:41:44 2006: DHCPREQUEST on eth0 to 255.255.255.255 port 67
Mon Sep 18 12:41:44 2006: DHCPACK from 192.168.1.1
Mon Sep 18 12:41:44 2006: /etc/resolvconf/update.d/libc: Warning: /etc/resolv.conf is not a symbolic link to /etc/resolvconf/run/resolv.conf
Mon Sep 18 12:41:44 2006: bound to 192.168.1.100 -- renewal in 1800 seconds.
Mon Sep 18 12:41:44 2006: SIOCSIFADDR: No such device
Mon Sep 18 12:41:44 2006: eth1: ERROR while getting interface flags: No such device
Mon Sep 18 12:41:44 2006: SIOCSIFNETMASK: No such device
Mon Sep 18 12:41:44 2006: SIOCSIFBRDADDR: No such device
Mon Sep 18 12:41:44 2006: eth1: ERROR while getting interface flags: No such device
Mon Sep 18 12:41:44 2006: eth1: ERROR while getting interface flags: No such device
Mon Sep 18 12:41:44 2006: Failed to bring up eth1.
Mon Sep 18 12:41:44 2006: done.
Mon Sep 18 12:41:44 2006: Initializing IP Masquerading...IP Masquerade has not been enabled in the kernel.
Mon Sep 18 12:41:44 2006: done.
Mon Sep 18 12:41:44 2006: Loading IP Masquerade kernel modules...done.
Mon Sep 18 12:41:45 2006: ^[]RSetting up general console font... done.
Mon Sep 18 12:41:45 2006: Setting up per-VC ACM's: /dev/tty1 (iso15), /dev/tty2 (iso15), /dev/tty3 (iso15), /dev/tty4 (iso15), /dev/tty5 (iso15), /dev/tty6 (iso15), done.
Mon Sep 18 12:41:46 2006: ^[[9;30]^[[14;30]Running ntpdate to synchronize clock...done.
Mon Sep 18 12:41:57 2006: Initializing random number generator...done.
Mon Sep 18 12:41:57 2006: Recovering nvi editor sessions...none found.
Mon Sep 18 12:41:57 2006: Setting up X server socket directory /tmp/.X11-unix....
Mon Sep 18 12:41:57 2006: Setting up ICE socket directory /tmp/.ICE-unix....
Mon Sep 18 12:41:58 2006: INIT: Entering runlevel: 2
Mon Sep 18 12:41:58 2006: Starting system log daemon: syslogd.
Mon Sep 18 12:41:58 2006: Starting kernel log daemon: klogd.
Mon Sep 18 12:41:58 2006: Starting cvs pserver chroot wrapper: cvsd.
Mon Sep 18 12:41:58 2006: Starting MTA: exim4.
Mon Sep 18 12:41:59 2006: Starting internet superserver: inetd.
Mon Sep 18 12:42:00 2006: Starting OpenBSD Secure Shell server: sshd.
Mon Sep 18 12:42:00 2006: Setting up X font server socket directory /tmp/.font-unix...done.
Mon Sep 18 12:42:00 2006: Starting X font server: xfs.
Mon Sep 18 12:42:01 2006: Starting Xprint servers: Xprt.
Mon Sep 18 12:42:02 2006: Starting deferred execution scheduler: atd.
Mon Sep 18 12:42:02 2006: Starting periodic command scheduler....
Mon Sep 18 12:42:03 2006: Starting apache 1.3 web server....
Mon Sep 18 12:42:03 2006:
***********************************************************************************

the process by which I am recompiling is as follows;

install the source:
fred@debian:~$ sudo apt-get install linux-source-2.6.16
:~# adduser my_username src
bash:/usr/src$ rm linux
:/usr/src$ tar -jxf linux-source-2.6.16.tar.bz2
:/usr/src$ ln -s linux-source-2.6.16 linux
:/usr/src/linux$ cp /boot/config-2.6.15-1-686 .config
:/usr/src/linux$ make oldconfig
:/usr/src/linux$ make menuconfig
:/usr/src/linux$ fakeroot make-kpkg clean
:/usr/src/linux$ fakeroot make-kpkg --append-to-version=.060917 kernel_image
:/usr/src# dpkg -i kernel-image-2.6.16.060917_10.00.Custom_i386.deb

fixed:

I removed the following entries from /etc/modules
ide-cd
ide-detect
ide-disk
psmouse

rebooted and errors are gone
sicne all is working fine as I reported, then the above must have been hard compiled into the kernel, I just don't know why it did not update /etc/modules as well.