I'm not sure this will help, but if you have a situation where you are dealing with input and output file handles, and the corresponding "files" are both supposed to be gzip compressed, you probably want to try PerlIO::gzip -- it sets up (un)compression as a PerlIO layer:

use PerlIO::gzip;

open my $fh, "<:gzip", $gzfile or die "$gzfile: $!\n";
binmode STDOUT, ":gzip";

while(<$fh>) {
    # do stuff
    print;
}
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(worked for me on a simple task)

UPDATE: (2010-10-18) It seems that PerlIO::gzip should be viewed as superseded by PerlIO::via:gzip. (see PerlIO::gzip or PerlIO::via::gzip).