I'm not sure if this would work, but I googled and found where someone said to uncheck the the "Snap Vector Tools and Transforms to Pixel Grid" under the General section in Preferences in response to someone else posting that they were having the same issue.
Honestly, I've never had the problem you describe (I also use CS6), and that box is checked for me. So, I don't know if that relates to the issue you're having or not. Worth a shot though!
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