I checked on my three test-laptops with several mice and I can't reproduce what you are experiencing.
Since the USB ports are completely owned by the kernel and the mouse routines by the Xserver I very much doubt that the problem is the MATE-desktop.
Although I strongly suspect a conflict between the newer kernel and your hardware, I advice you to file a bug here anyway:
One thing left to try though: You can completely disable USB powersave in the kernel. The following link explains how to do that:
If this doesn't work then the problem is probably something else, though at the moment I can not imagine what that could be. 