Actually, I’m looking through the change logs, and it looks like there was a fix for “Fixed monitor index corruption on Windows” which could explain things.
I’m assuming you have CRU on your system? If you don’t, you really, really need that for CRTSR. You have to go in and delete all the resolutions for the CRT that you don’t want and create detailed resolutions for the Native Res’s, and then Standard resolutions and extension blocks for everything else.
There’s also a utility that is on the CRU forum that lets you delete all the scaled resolutions that Nvidia/AMD keeps throwing out weirdly. It doesn’t work with Intel.
Assuming you already did all that, try going into CRU folder and resetting the monitor indexes with the included utility.