Just a wild guess. Have you, by any chance, installed a program named rmdir.exe (e.g. from UnxUtils) a couple of days ago?

AFAIK, it would be called (when found along PATH) in place of the cmd.exe built-in rmdir, but would presumably choke on /S /Q... — see Windows: system("type ...") vs. system("cmd /c type ...") for a similar case.