Here's an example url: http://www.theoldcomputer.com/roms/down ... VzLnppcA==
It's heavily reproducible in Chrome. The fix is pretty easy, provided you have access to the codebase. The problem HTTP header is this:
Content-Disposition: attachment; filename=Legend_of_Zelda,_The_-_Special_Edition_(Zelda_Hack).nes.zip
It should look like this (note the added quotes):
Content-Disposition: attachment; filename="Legend_of_Zelda,_The_-_Special_Edition_(Zelda_Hack).nes.zip"
So the code should look something like this:
add_header("Content-Disposition", "attachment; filename=\"" + $filename + "\"");