The jacob1's mod window bug (above) strikes again!
"Help! Whenever I open the mod, it stays minimized! If I try to click on the icon in the task bar, the window does not pop up. It still shows a preview of the window."
I figured out what caused it; whenever you disable a script in the built-in script manager and it askes you to restart the application, if you click done, it restarts and causes the bug.
This time, changing the type of window the mod opened in did not help, but deleting powder.pref did.