We discovered the problem, but forgot to update this page as a reference for others. By looking in the file /tmp/niSystemReport.out.gz, we were able to find more information regarding why the install was failing. NIKAL is a kernel module, and it was complaining about version magic numbers disagreeing between itself and our installed kernel source in the line:
Sep 26 12:11:01 ctl2121 kernel: nikal: version magic '2.6.12-31mdkcustom 686 gcc-4.0' should be '2.6.12-31mdk 686 gcc-4.0'
So after searching around a bit, I found that the kernel source we had installed was set to this 31mdkcustom, whereas nikal was expecting 31mdk. So we went to the Makefile for our kernel source found in /usr/src/linux, and edited the fourth line from
EXTRAVERSION = -31mdkcustom
to
EXTRAVERSION = -31mdk
Then, we recompiled the kernel source, by running make in this directory, then retried installing nikal with no problems, as the version magic numbers were identical. I'm not sure why the version was set to custom in the default install of the kernel source for 2.6.12-31, and my only worry is that it might cause problems if we try to install other kernel modules that expect the custom version magic number, but my guess is that it won't. What kind of weird kernel module *wants* to have a custom version magic in the kernel? None, I imagine.
Thanks for the response though, and I hope this helps other people in the future.