Usually, Cygwin Perl is the one that has less problems with IPC as the cygwin layer takes care of most of them.

Also, the most common cause of the rough edges is that Perl built-ins are modeled after Unix, so, another option, is to rely as much as possible on the Win32 API. Unfortunately, the wrappers you may find on CPAN (Win32::*) don't always have the quality one would like. Your mileage may vary.