I currently have a 2005 jetta gli with the 5sp tiptronic and the same exact issue.
I recently changed the fluid and filter as well and its not as bad as it was(might be my imagination), but still when shifting from 2nd to 3rd it hesitates and then will jerk when 3rd engages unless i shift up from 2nd and then let off the gas and wait until the rpms go down then if I slowly press on the gas again it will shift smoothly but is obviously an issue.
The check engine light is not on either. Correct me if I'm wrong, I'm no professional mechanic, but i would assume a scan would be clean if the light isn't even coming on. I had the problem with the N92 solenoid already that kept me stuck in 1st gear when cold before it would shift, but the CEL was on then so I had it scanned, swapped the solenoid, and it was fine.
I unfortunatly don't have a solution for the current problem yet but I would really appreciate one as well since it's quite annoying.