Can you show us a short HTML example and a short Perl program that exhibits the problem? I have not encountered problems with POST data, CGI and Perl.

Also tell us what webserver you are using and whether you're talking about the module CGI.pm or the Common Gateway Interface.

Also maybe read the documentation on mixing POST and GET parameters. This describes a problem in the other direction, GET parameters getting shadowed by POST parameters, but maybe that helps you find the real error cause.