It has been a while since I've used Windows, but I do recall one thing that could cause this in many different systems that may be the problem.
It almost sounds like you've got Hot Corners acting up. Contrary to the name, it has options for sides as well as corners. Basically, it sounds like your computer registers a command to go to sleep when the mouse goes over there, then when you touch anything, it then tries to wake up, interrupting itself, making itself feel grumpy without its cup of coffee, and pausing while it reorients itself and lets you continue on itself.
One potential wrinkle to it is that part of the system thinks hot corners are up and running, and part of it doesn't. These two parts argue with each other, eating up all the system resources, until the matter finally gets resolved and you can continue with your work.