I believe that someone once told me that the memory dedicated to an array doesn't shrink, even if you assign an empty list to it -- rather Perl just adjusts its pointers for the start and end of the array, but the memory stays allocated. Could that be causing the problem?

You might try using a new lexical array or array reference instead of "cleaning" the array and see if that helps.

P.S. That's true for hashes as well -- while the memory for the keys and values can be cleared, the memory allocated to the underlying array stays allocated. I think that jdhedden told me that when we were discussing hash-based vs array-based inside-out objects.