I switch between using tortoise git and cmd line git on cygwin very frequently, and lately I've noticed that when I git status via cygwin and no changes are found, then I go to use tortoise git, and right click on a repo then use the "Git Commit -> ..." menu item, I get a list of files that have supposedly changed, but of course when review the diff there are no changes to the file contents, it's actually the file permissions which appear to be changed, which git via cygwin does not recognize.

So what is wrong with my tortoise git setup?