FTWiener: Alright, so I found a fix that works on my system. I'll post what I did in case somebody else is searching online for a solution.
Basically, I just ran the executable in both windowed mode and emulation mode

So create a shortcut for the main game's executable and right click on it.
Look at the text field that says target. For me, it looks like ""E:\GOG Games\Sanitarium\sntrm.exe"

To the end of that address, add "-w" for windowed mode and "-e" for emulation mode.

Final result should look like this:
E:\GOG Games\Sanitarium\sntrm.exe" -w -e

After that, run the game and feel free to resize the video to your approximate desktop size. Not quite fullscreen mode, but it'll do.

Good Luck

djknightime: Another solution to the flickering that worked for me was to go into the Nvidia Control Panel, add sntrm.exe to the "Manage 3D settings" menu, then disable Vsync. I'm sure AMD has a similar option, but I don't know where it'd be.

As for the cutscene crashing, try adding a DWord key in your registry called "SoftwareOnly" and set it to 0 (or if it's there and set to "1", change it to "0").

Check these two locations for it:

HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\Microsoft\Direct3D\Drivers

HKEY_LOCAL_MACHINE\SOFTWARE\\Microsoft\Direct3D\Drivers