pelagic,
This is just a hunch, but was your perl compiled for large file support?

$ perl -V
Compile-time options: MULTIPLICITY USE_ITHREADS USE_64_BIT_INT USE_LAR
+GE_FILES PERL_IMPLICIT_CONTEXT
[download]

I am going to go check perldelta now to verify your version supports large files even though it would require recompiling.

Cheers - L~R

Update: Large file support became available in 5.6.0. You may have to resort to letting the OS handle it for you.