We're trying to reproduce this with the hardware we have. No luck so far, but we have some new questions.
Can you post your user.cfg.xml file from your configuration directory? We don't think the problem is config related per se, but having this file answers a lot of questions about tool window docking all at once.
Do you have any mouse or touchpad customization or macro applications installed? I'm thinking of things like BetterTouchTool or Swish as representative examples. If so, which ones do you have?
You mentioned some of the toolbars and windows you've been using. Do the mouse problems only start when using particular tools, or does it just seem to be random when the problem starts?
If we can't reproduce this here, our next step would be to provide you with a debug SlickEdit that has added event logging so we can try to see what events we're getting leading up to the problem.