Off the top of my head....
if you're comparing Linux file to PC file, you'll find CR/LF on PC and just LF on the linux files. That would give you a binary difference that wouldn't show as a textual difference.
Somewhere there's a command to look at file format (PC or Linux). I'm not sure where it is, though.
If you're looking for non-text differences, when you invoke the VS diff tool, choose the option for NOT using source diff. Source Diff ignores whitespace (and will tell you things like tabs and spaces are equivalent). NOT source diff will highlight every difference.
HTH.