Ah, ok.
With a manual valve body there is no way the line pressure can be adjusted for temp changes, so when it's cold on the road there will be changes to the shift pressures and times that can't be accounted for due to the lack of a TCU. I hope you at least have a thermostat in the trans cooler lines...
As Greg mentioned above, a PCS controller is expensive but it changes the way the auto drives substantially, and allows infinite adjustment via a laptop. I was surprised how well his car drove, better than a manual or DSG I thought, and I usually hate auto's.