Being that no one has chimed in with an opinion, I might as well. I am not sure with the tranny you are using, never seen one but i will hazard a guess as to the cause. Assuming the clutch is releasing all the way the only other thing i have seen which may be similar is the "selecter" on the synchro assy (the outer ring that is attached to the shift fork) i have seen one that had a peice of the synchro dogs that went inside and damaged the splines where it rides on the hub, actually i think now it was the hub that was damaged, had a mushed area at the end that made it hard to get into and out of gear. This only affected 1 gear however, not 2, but being 1-2 should be on the same hub it may be possible. My guess for a cause was someone not having it all the way in gear before letting out the clutch under power.
Let me know if i am close and good luck.