You didn't say what year it was, but some of those transmissions are known for slipping in and out of gear. Once they start, the 'dogs' on the piece between the bevel gears that connects the drive from the bevel gears to the shaft get worn and damaged and finally they geat so they just sit and klunk and don't move much at all.
I think the problem starts with either of two things: 1. Too agressive in pressing the motion pedal (shafts have to turn up to 120 degrees after shifting the direction handle and before the dogs engage the gears and can really be flying when the parts finally align if the operator stomps the motion pedal.)
2. The other problem is the fit of the gears themselves. On the one unit I took apart the bevel gears had what I thought was too much play on the shaft.
To even begin to fix one of these transaxles, you need to replace both bevel gears and the piece between them and the shaft they run on.
MTD does have an update replacement transmission kit that seems to be more durable than the model that gives the most trouble.