I should be doing marketing for this place, if it didn't market itself. From
Wes Haggard. I was too lazy myself to figure this out, but he's gone and done it for us.
Under [HKEY_CURRENT_USER\Software\Notepad2\Settings] you can add a new DWORD value with the name "ReuseWindow" and give it a value of 0. This will have it open a new window by default.
Thanks Wes!