I can't say I've noticed it, but then I only tend to shift pitch a tone at the most.
You might try applying some EQ before or after you shift the pitch. You should have an EQ filter built in, but if not you can download one as a plug-in.
Never had any problems with windows. Had a similar problem with my Mac until latest version seemed to cure all in fact have just changed pitch down 3 semitones for the Aebersold Autumn leaves for a workshop with no problems at all.