I'm using White Box Enterprise Linux (which is compiled using the Red Hat Enterprise Linux 3 source). It comes with the 2.4 kernel. I decided to upgrade to the 2.6 kernel. I edited the kernel script, compiled it, etc. but when it booted a good portion of the modules didn't load. Here's everything I did:

make xconfig (edited it and saved it)
make bzImage && make modules && make modules_install
cp <linux source>/arch/i386/boot/bzImage /boot/bzImage-2.6.9-selinux1
cp <linux source>/System.map /boot/System.map-2.6.9-selinux
rm /boot/System.map
ln -s /boot/System.map-2.6.9-selinux1 /boot/System.map
//Edited the grub.conf file

I compiled ext3 support into the kernel and everything else I needed to boot so I didn't need an initrd, I even compiled fat32 support into the kernel and that didn't work once I booted up the system. I heard that I needed to install something called modules-init-tools before I did the kernel upgrade however I didn't, do I need this? Also why wouldn't fat32 work when I built it into the kernel? I also heard you needed to load modules you want to boot with in the system in /etc/modules.autoload.d/<kernel version> However I don't have an /etc/modules.autoload.d folder even in my default system. Since this is technically a Red Hat system does Red Hat store this info somewhere else because I would assume I'd have a 2.4 file from the old kernel if not. I just have an /etc/modules.conf and /etc/modules.conf~ file.

hi
You do if you get a 'QM_MODULES: Function not implemented' error when trying to use insmod, modprobe, lsmod etc
It is possible to install this post compile . .

Are you sure that the fat32 support doesn't work, or that perhaps the error you see is the system looking for the old fat32 module in the modules for 2.6 ?