perl 5.6.1 is ancient. Seven years is a lot of time in software land. If you can, try to upgrade to 5.8.8 or even 5.10.0.

There were many fixes for memory handling since 5.6.1, and I wouldn't bother chasing bugs in perl that might have been resolved years ago.

I honestly don't know if that will fix your problem, but I still consider upgrading worth the effort.