Just a WAG - is the parking pawl fully engaging? 
My 08 passion finally burned a valve after 130K and I plulled the engine for a ring and valve job. After reinstalling the engine, I reconnected the battery and attempted to go through the transmission re-learn procedure and encountered problems. First, let me add that I started with the transmission in neutral, ( I had previously put it it in neutral so I could move it a little while getting ready for engine removal.) You are supposed tostart the procecedure with it in park,but no matter what I do, I cannot go to park. I can go from neutral to reverse or drive, but not to park. At one attempt, at the beginning, I heard a few of the gear-moving noises, but not as much as I remember hearing the last time I did it several years ago..I re-checked the connector plugs to the transmission and the little ball-and-cable connection and can't find any problem there. Don't know where to go from here..Outof desperation I tried disconnecting the battery and waiting about thirty minutes but nothing changed.Also, I don't get any trouble bars. ;Any suggestions gladly appreciated..