Debugging with CLion in Cygwin bugged?

I'm trying to get a project of mine to run on Linux, as well as, Windows.  I got to the point where I can compile, and run some of the code successfully on Windows, before crashing.  The only thing is when I run a debug build arguments don't pass to main correctly. (I get a bunch of garbage nonsense and argc is one less)  Also, instead of having the build startup in CLion's command prompt it opens in a separate Windows command prompt.  Is this a known issue?

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CLion: 2016.2.1

Cygwin: DLL 2.5.2

GDB: Cygwin 7.10.1-1

CMake: 3.6.1

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