Disconnect the door from the opener and lift it manually. In fact ask your wife to lift it. I think you have repaired the results of a door problem. I know you said the door isn't binding but I am concerned with the weight of the door. It really isn't normal for the door to stop after a few inches on the way up and then reverse. This is a symptom of a very heavy door.

thanks Don for the followup. I thought about the heavy
door issue to, but the opener acts this same when even when
I disconnect the chain from the door, so I am sure it is the opener. It has been working well for about 20 years.

I also replaced the gears in my opener and its doing the exact same thing. It goes up about a foot the goes back down. I know the door isn't too heavy because it worked for 5 years. I also disconnected the door and the bracket only travels about a foot then goes back. Anyone know what else I should try?

Loosen the chain so you can remove it from the small sprocket on top of the motor housing. Run the unit until that sprocket turns counter clockwise and then stops. With the door in the open position replace and tighten the chain. You will probably have to make minor adjustments on the up and down limits on the side of the unit but this should get everything in sync again.