Which desktop are you using? For KDE, there is a helper service involved that could be involved. If you see a requester popup when inserting a pen drive, it is probably working. I assume the same is true for Gnome.
Also make sure that the hald, udevd, resmgrd & dbusd daemons are running. Check your kernel boot options in /boot/grub/menu.lst. You need acpi enabled for dbusd to work.
Also check if /etc/resmgr.conf contains the lines:
# generic libusb access
Also verify that you can mount the pendrive manually as root. If there is a problem with the filesystem on the drive, you won't be able to mount it. Also remove any entries for that device in /etc/fstab. It will take precedence.
Before trying to automount the pendrive, in a terminal, like konsole, enter:
sudo tail -f /var/log/messages
Then insert the drive. There may be further details on why it isn't working.
There are also a couple of files; /media/.hal-mtab and /media/.hal-mtab-lock. When the device isn't mounted, it shouldn't be listed.