I believe the shifting issue is due to the TCM which has been addressed.I bought the Flashzilla and the Malone stage 1 for my 3L TDI Cayenne last month. I already have the TCU reflash, although I still have a DTC until I can figure out how to recode it.
The stage 1 is rather underwhelming. Up to 90% accelerator pedal it drives exactly the same as the post fix calibration. It still has the same drivability complaints during normal driving as the regular post-fix calibration. I really don't want to delete all the emissions just to make it drive like it used to. FE is also unchanged with the stage 1. The torque increase is noticeable and makes it a bit quicker, but not mind blowing.
In hindsight I'd save the $750 (FZ + stg 1 cal) and just keep it stock. I sent Malone a few emails asking about the changes and they were rather coy as to the drivability changes; now I understand why.