It sounds likely to be a software issue with APT, particularly if it only started after upgrading. It's not a known problem to us, but have you also tried asking on the APT forum/support in case other people are finding similar things?
One thing you could try is using the camera with Artemis Capture and seeing if it does the same thing. If it does, I'd try another USB. If it still does, then it's sounding more like the camera and you might be best dropping support@atik-cameras.com an email. But it sounds like APT is the place to look first!
Let us know how you get on,
Jo