One of the last NVDI update files floating around has always given me issues.
Think I've stuck with 5.03 or lower. If you have a working NVDI with the correct sys files and, since using MiNT, correct paths, all should be golden. If NVDI is missing sys for the color depth you have set, it will looked jumbled, just as if they were missing from a Falcon video card installation. Delete your old desktop.inf file while you're at it. It's near "plug and play", the xcontrol and xboot are discussed at length in the CT is having issues section. I've booted the CT and SV using Atari's original MultiTOS disk, swapping out XControl and all works perfectly, with the ability to change SV resolution from the Falcon desktop.
Buffer. Sure leave it off if you don't care about bad SCSI writes......The buffer and CT and not specifically related. Rodolphe may of had one or two Falcons, with 3 or 4 developer group. There's a chance those Falcons did not need a clock patch. I'm betting the 1000 or so still in existence do. That, or Rodolphe didn't bother with continuous writes to the end of the bus where the SCSI IC is..
You can tell I'm a "clock patch" fan