Don't worry about it; it's normal.
From what I can tell, there is a change in rendering in v2.1 indeed: TG2 now "hammers" the CPU more aggressively (which is a really, really good thing). In Windows (and other OS's as well), by default, the "active" window gets multitasking priority. So when the rendering window is in front/in focus and "active", there will be very few CPU cycles available for your mouse driver (or anything else, for that matter).
Simple solution is to click once somewhere outside the render window or the TG2 interface (like the desktop, for example). Then the OS will focus on that, and give the rendering window lower priority. But don't worry, it won't slow down that much, at least for simple operations like internet browsing, etc - I do it all the time while waiting for previews.
The same thing happens with many CPU-intensive applications/operations, and especially with modern input devices that use "heavier" drivers and resources. Pen tablets, in particular, are notoriously affected in such cases.
