I know the focus of the post is to do a dual boot, but there is a lot of useful information in it, and, as I said, the recommendation is to use legacy mode, not UEFI.
@darkmage Is your hardware an Rpi3 or an Rpi3 +?
Have you tried another SD card?
As said @voljega is important to turn off the correct way, shutting down wrongly corrupts the system. Doing a disk check on windows often solves the corrupted system problem.
