Linux usually tries to use all available memory, then it starts to using swap. By reading your description, looks like the process is being killed before that.

My only guess is that the Linux box is using a compile version of Perl that may not be working fine, or the modules you're using may have an specific bug. Anyway, looks like an issue more related to C code than with Perl.

Maybe you can use perl -dDprof in the Linux box with a smaller set of data and see what happens. If the program is not killed, you may be able to identify where the program is consuming so much memory.