You mean even if you click on it, it doesn't appear? Even though the window seems to be open on the taskbar?
If you can find your powder.pref, look for the WindowX and WindowY parameters. If any of these is too big (in the range of thousands) or too small (negative), try setting it to 0, save the file, close it, and try opening TPT afterwards.
That doesn't sound like a TPT issue, generally. It shouldn't cause your PC to freeze after any amount of time. Even doing something extremely laggy will just give you a popup eventually as your OS decides to kill it.