It's weird that this works for gzip files, indeed. But... I suspect that the problem is with the -l command line option: I'd probably get rid of this and, as an added bonus, set binmode(STDIN) before the print. Chances are that it's a problem related to the different approach of Win and *nix to newlining.

Moreover, I see that md5_base64 expects a scalar as input, so I suspect that you actually wanted to activate slurp mode in order to read the whole file at one time. In this case, you should set $/ to undef before reading.