Just read this on a ebay site that was selling a GSA. Any thoughts?
 
After any work is performed on the SMT system it must be fully bled and reset, then the relearn procedure must be performed. A Toyota dealer tool (or compatible TIS cable available for purchase on ebay) is required for this relearn. If you fail to reset the SMT TCU after a parts swap it will not function properly.

They also say the same thing when you do a clutch change on them.  'Parts Exchange' is the term that comes to mind.  However, I know that this is not always the case.  Much of it is to do with the selector shaft being in the exact neutral position when its all bolted back together - Toyota even make a special service tool to help with this particular task: a piece of plastic, haha.

Thank you so very much for your reply, it was most helpful and best of all, worked!