Just a thought, but is the system using all of the same hardware (i.e., hard drives) that it came with in 2002? 10+ years is a long time, and it's possible this is a hardware issue and not simply a RHEL 3/Perl issue. I had odd issues with Perl when a hard drive controller died on one of my systems awhile ago, producing a corrupted filesystem; it might be worth checking on the drive health.