Sorry, but I have never come across a problem such as you are describing. Unfortunately, without being able to reproduce the condition and because it is very intermitten, it will be hard to track down until it gets worse.
Only thing I can think of at the moment would be to double check the spindle encoder, belt and pulley carefully. The pulleys are made of aluminum and will become worn and/or distorted which can cause belt failure and inaccurate readings.
Good luck and keep us updated with anything you find.