Did you buy a new motor for it or salvage something? Was it the exact model you replaced?
I am curious about this because my TGCD setup has a hard time with Sherlock 2 once in a while and I've adjusted and adjusted and so on...
Mine also will not load back-ups of Super CDs but seems to have no problem with regular CDs...
It was a new one, exact model matching. Motor shaft was a little longer though than the built-in. I had to shorten the middle pin on the magnet, that is matching into the top of the spindle for it work perfectly.
I recommend you get yourself a new motor, I would step away from salvaged ones - you never really know in what condition they are. Looks like you´re having the same problem as I had...so