Yes, this is a weird question, but I promise this is what is actually happening. It's 100% repeatable every single time.
I've got a MacBook Pro with El Capitan, and hooked up to it I have a Logitech Performance MX mouse with a 2.4GHz wireless receiver. For about the past two weeks, whenever I close Chrome my mouse completely stops responding. I've waited up to 5 minutes and the mouse never responds. If I unplug the wireless USB receiver and then immediately plug it back in, my mouse will start working immediately... at least until the next time I close Chrome.
You might ask, "why would you close Chrome then?" Well, I wouldn't, but I'm a web developer. As part of my grunt build process Chrome is launched to run karma unit tests. There are times when I need to use Command+C to stop the tasks. This of course closes Chrome and then my mouse stops working. If I manually close the browser karma launched (without stopping the grunt process) the mouse also stops working.
The problem is unrelated to grunt/karma because if I close the Chrome browser I'm writing this question in -- a browser I manually launched -- my mouse also stops working. It ONLY happens when a Chrome process completely stops. I can close tabs without affecting my mouse. I can open a second window and close it and my mouse works just fine. I can open an incognito window and close it, and my mouse is also fine. If I close the last open Chrome window though my mouse completely stops responding immediately.
I can close any other program and the mouse also works just fine. I should also mention the built in touchpad never stops working... but I keep the MBP lid closed almost all the time.
I probably end up starting and stopping my grunt process 10-20x a day, and this has become a huge inconvenience (although one my co-workers find pretty amusing). Does anyone have any ideas on how to even begin to troubleshoot this?