We've had this same thing happen. What seems to be the problem is that some people will swipe the card after hitting the "credit card" button, but BEFORE the credit card window comes up. What happens is that the credit card window then opens BEHIND the main sales window, graying out the whole program and making it look like it's frozen.
This most recently happened with a new employee. I just scrolled through the open windows to find the credit card window, and all went well. After being instructed on the timing of the credit card swipe, the issue has not happened again.