Also when you run into it, if you do a single click somewhere on the MoI window does that then fix it?

Yes it does! but its still annoying... but I think I've found the problem! I have < as a shortcut, the problem happens after I use that key.

I do have a shortcut assigned to the - key, but if i press one of the other shortcut keys while a tool is active, the tool of that key becomes active.