Update: none of below applies, since Windows doesn't use glibc.

What OS is this? I wonder if you are hitting the pathological-free bug with an older glibc.

Update: the bug I'm thinking of is in glibc 2.2.x where free calls will suddenly start taking an enormous amount of time and cpu. If I understand correctly, the malloc library was rewritten for glibc 2.3 and the problem no longer exists there. If you have a glibc 2.2.x, make sure perl is built to use it's own malloc (Configure with -Dusemymalloc) or upgrade to a newer glibc.