I have the same issue. My MK4 VR6 Jetta with automatic transmission started doing the same weird shifts and but i continued using it for a few more days until it stopped even changing gears . My bad... It would start when I turn the engine off for a few minutes, and then it would take the gears again after i put it in drive. So I went a head and checked it with my VAGCom scanner and I got a few sensors off and a fluid sensor as well. Since I didn't have many options to take my car to so I had to take it to the dealer(i knew it was going to be painful); they said that my transmission was gone and I needed to replace it; $4500. I couldn't pay the amount of money so I took it out of there and towed back home while I think what to do.
Long story short, is that some other people have made me other quotes that go from $400(labor) to 900(labor), but I need to get the transmission(which I don't yet know where to get it--any thoughts?--) and others charge me form 4500 to as low as 2500, putting the transmission.
I haven't done it and I need some advice. I know Nothing about mechanics, but one thing for sure is that I love my VR6. Please HELP!