TMCC Problem

Are you running TMCC or Legacy on the layout?  If you're running Legacy, and you changed the address of the locomotive, check to make sure it didn't get set back to Legacy control in the CAB2, it won't run that way.  This bit me when I first got my Legacy system.

Johns right. It bit me also.

Ron

No Just running TMC

Do you have two tmcc bases? Just grasping at straws but if they are both powered up could it be "confusing the loco? It has been mentioned on the forum before that once a TMCC base is plugged in you could theoretically run a train in any room of your house as one side of the signal is transmitted via the house wiring ground. Even though the "workbench base" is not connected to your layout your loco may be waiting to respond to its signal. You could also try switch the "bench" base with the layout base and see if that works.

I've seen the workbench TMCC affect the Legacy in the same room, haven't tried it across the house.  It's good practice to power down any other TMCC/Legacy command base and only have one powered.

Moved the work bench tmcc base to the layout evrything works fine. Tried the other base on the work bench will control other loco's but not the Atlas GP9. For now that works for me but I would still like to find out what went wrong!!!! 

Sounds like the one command base has a problem of some sort.  Look at the bright side, progress!

Could be that the "bad" Base is tuned a bit off to one side compared with the other Base and the GP9.  See 'Command Base Signals' near the end in http://www.trainfacts.com/trainfacts/?p=298 for the tuning procedure.  In your case, you will need to check the tuning with both the GP9 and your other engines to see that they all will work.