It's important to verify that you're not having any plug-and-play type of events associated with this issue. If any indicator L.E.D.s, including the mouse's transmit diodes, happen to cycling on/ off. You could simply be having connectivity issues/ possible defective mouse. If your mouse cord did twist up a bit, you could have a defective cord on the mouse.
Cleaning the optical path can cause the same sort of symptom, however, the indicator L.E.D.s will stay lit, rather than cycle on/ off as mentioned above.
Are you running multiple GPUs? It is possible that a driver is responsible/ or hardware changes with existing architecture led to this. It is potentially possible that an updated USB 3.0 driver is the culprit. This issue comes up when PCI Express Lanes are reduced by GPU consumption, not allowing the USB system to those lanes for use, which they need, forcing them to down-grade to low async speeds. Imagine your high end mouse trying to send all that data across 128K connection, it is a substantial overrun of data.
If you can post your configuration? Remember that if you're on X99/ 2011, that's all I need to root out USB driver issues.