My Affinity with the 4000 Allison did something similar, went into 1st gear and stayed there awhile. Couldn't shift it at all. Then for a while it worked fine. Then wouldn't go into reverse, neutral or anything, then worked ok for a while. Usually required a shut down and restart of the engine to work again.
So.... I took it down to the CAT / Allison dealer and they hooked up the reader and it spit out a fault, and it was a bad output shaft speed sensor, I think. Anyway, $280 later all was swell. No problems since.
Seems, so the dealer said, that if the transmission doesn't know the speed (rpm) of the engine, it won't let the transmission ruin itself.
Anyway, that's my story and I am sticking to it.
01 Country Coach Affinity 42 Enclave Toad
Lilly the Raschon and Lulu the Terrier.