Good news everyone!
I ran into the issue again while switching to a better video card, and this time I found a solution! If anyone else ever runs into this problem, here's what you do:
Open the registry editor (win+r and type regedit)
Goto HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Video\
There will be many folders with long and confusing names. Open every single one of them.
You need to select each and every one of the subfolders called 0000. Create a DWORD in all of them named "DigitalHDTVDefaultUnderscan" and leave all those new keys at 0.
Reboot.
Tahdah! I have no idea whether you need to put a key in for every 0000 folder or not, but I'm so far experiencing no negative side effects of having done it this way.
Side note; never use the /setmax option of Nirsoft's MultiMonitorTool. It will permanently break your refresh rates and you will need to reinstall CRT Emudriver just to get your 15khz video to stop tearing,