2004 Saab 9.3 2.0T problem shifting in first and second after driving for 30 minutes

Has 118,000 miles and we have replaced speed sensors and changed transmission fluid and updated computer software. It runs perfectly for 30 minutes whether driving in town or highway but then hesitates and jerks when shifting from 1st to 2nd and downshifting also. After it shifts into 3rd, it is fine. Repair shop says it could be gear box or computer problem. No one in town seems to know what it is for sure.

Gearbox? Manual trans? Computer involved means auto? Valve body, shift solenoid?

Automatic 5 speed high pressure transmission