Not entirely true, Larry. If he *were* to remove that installation of MKS, he would then discover that his Rational Rose/Clearcase/Clearquest installation was broken. IBM's Rational toolkit relies on having those MKS tools available (and no, they cannot be coerced into using cygwin's tools instead).
I don't use Clearquest, but I use both Rose and ClearCase and I didn't installed at all MKS.
Anyway I had the problem described by the original poster when I installed Rational Rose the first time because I choose to install "Quality Architect" (if I remember well), removing that component I haven't had no more problems with Cygwin.
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