It is possible to have two versions of GCC to coexist: the native windows MinGW version and the cygwin linux version? Things get problematic when on Cygwin the system tries to compile with the MinGW version of GCC, and vice versa. How can I keep both versions of GCC?
Psychic debugging suggests you have one or both in your global path. Take both out of your global path (gcc should yield "bad command or file name" or similar run directly from cmd.exe) and set up the shortcuts so they load the proper environment for each.