I don't use MinGW64 and have only VC200x (don't know exactly) installed for testing purposes on onbe of my virtual machines.
But on my debian system I use several versions of gcc 4.1, 4.3, 4.4, 4.5 (all 64-bit) mingw32-cross-compiler, compiler-scripts using ccache, gdc and I can switch between them flawlessly, even if I just have created (copied) a new compiler.
So I wonder what happens for you.
One question that just comes in my mind: do you use a project or do you try to compile single files ?