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 c
I have both of them installed and coexisting peacefully. Cygwin is installed in c:\cygwin while MinGW is installed in c:\msys\mingw. I didn't have to do anything unusual to make them coexist since their environments are set by their respective startup shortcuts.
There must be some specific step in your installation that caused them to become coupled in some way. If you describe your installation sequence and locations perhaps someone can offer additional advice.