How did you save the window?
How are you opening the new window?
(Which menu items or actions, and what are those actions configured to do in Preferences, if applicable.)
If you're seeing high CPU usage with Opus, send us some process snapshots made during the heavy usage and we'll take a look.
Do you have anything installed that might be modifying other programs' windows? Anything that changes the way other programs look, or adds elements to window titlebars, or that helps move/resize other programs' windows?
There is no way that Opus could affect your keyboard, especially after a reboot and before you've even logged in.
That kind of thing sounds like a more general issue with the computer or drivers, or even a loose cable.
Whatever's causing that may be involved in the other issues.