A couple of things to check. First is clutch pack set correctly at .090 to .120". If it is set too loose and slipping too much then it will not lock up at the shift. If it doesn't then most likely the clutches are burned. If you open the fill plugs on the top and stick your nose close you will be able to smell the burned clutches.
Second. Make sure the forward cover over the spray gas the gap in the down position. In any other position the transmission will not shift.
Lastly is the setting of the slack in the clutches after the transmission gas been assembled. Matt Moore at Lenco showed us how to do it correctly and we have never had a problem since. Here are Matt's procedures
1. Back off locking nuts on air pods and move lock nuts up high
2. Remove top oil fill plug
3. Look down oil fill holes at clutch ring and make sure there is a small punch mark on ring. If no mark then make one with a punch. Position is not critical as it is an eyeball reference.
4. Turn air pod clockwise while watching punch mark on clutch ring. You should see or start to see punch mark move towards the air pod. You nay need a flashlight to view this. You should also feel resistance in the turning of the pod at this point.
5. Once you see movement of the punch mark towards the air pod and turning resistance increase stop and turn the air pod counterclockwise until you see the punch mark move away from the air pod and the mark stops moving. At that point turn air pod one complete turn counterclockwise then lock the air pod nut down tight at that position.
6. It is not critical if you turn the air pod slightly less or slightly more. 3/4 to 1 1/4 turns.
7. Fill with required amount of oil Install fill plugs.