I've done some searching online but there doesn't appear to be a clear fix for this.
Running GoG Control Ultimate Edition using DX12 from launcher.

Whenever I quit it forces me to start from the beginning of the game, because it's not saving checkpoints. Is there a fix or workaround to this?

It also isn't saving my interface preferences for increased mouse sensitivity and inverted vertical axis.

Ah. Resolved it.
Windows 11 is protecting User folders like Documents where game saves are supposed to sit.
Allow the app to access the protected folder from Windows Security > Protection History.