Change TCM
 

I had tranny problem for a while (2 months?)
During that time, I flushed ATF. At this time, it seemed that the problem was solved, but occur again.

Sometimes, these things were occured.

-AT light & CEL are on.
-When going into D, it start with 2nd gear, not 1st.
-Going to R, car bucks. there is heavy shock!
-When shifting up to 4th & down to 3rd, another shock.

First time, local mechanic found code P0772. After he reset the code, all symptom had gone away. (suspected some electronical problem, that is some controller.)

A few days later, AT & CEL was turned on again, so I went dealer.

They also found P0772 and another code P0742 was found. dealer said (TCM)Transmission Control Module had been shorted out.

They replaced it & flush ATF again. (On My Dollars!!!)

I picked up my mazda3 yesterday.
I hope... no such a problem again~!

what year, engine, & mileage is your ride?

I've been in terrible time again... Same problems again, finally, dealer said I need new tranny or rebuild it. TCM was a part of problem.

2006, 2.3L, 106000mile

P0772 - Shift Solenoid E Stuck On = http://engine-codes.com/p0772.html

P0742 - Torque Converter Clutch Circuit Stuck On = http://engine-codes.com/p0742.html

Both of those can be caused by contamination / rust / etc... in the trans, or maybe the TCM shorting out. Though if a new TCM didn't fix the problem I doubt it had anything to do with it.
SO they now say it needs a new trans - if you do that and it doesn't fix the issue, they should be responsible for fixing whatever the problem it is on their dollar. Its not your responsibility to hand over money when they didn't know what the problem was.

I'd guess that the trans flush is what helped, and there is just enough gunk built up in the solenoids that can't get flushed out fuly. In which case pulling it apart and cleaning it should fix it - but that's a lot of $ to pull it apart.

Concerning a rebuild - if that's the only other option, try some of the over the counter fixes at the auto store. You don't have anything to loose since the trans may be dead at this point anyway.
106k miles shouldn't have any problems with the trans, assuming that it had its fluid changed on schedule.