For what it's worth, I had some car interface issues that seem to have gotten resolved by restoring the Touch. (Restoring can be a pain, but worth it if it corrects the problem.)
I have a 1G iPod Touch, OS 3.0 and a 2005 MINI iPod interface (I believe this is the first version of the BMW iPod interface.) When I first got the Touch I had some issues with each release, then things really smoothed out with 2.2.1.
After upgrading to OS 3.0, I went a couple of weeks with no problems at all using the 1G Touch in the MINI. Then for the last couple of days, after connecting the Touch to the MINI car adapter, the Touch screen showed the battery charging and when I switched the stereo to iPod mode, the Touch screen displayed the 'play' arrow. The MINI stereo displayed the "Checking CD" message, but never played. (This is a normal message but it used to display for 3-5 secs, then start playing.) My husband has a 2G Touch with OS 3.0, it played fine in the MINI. We also have an old 3rd Gen iPod classic, it played fine in the MINI. My 1G Touch played fine using our other GM car and its interface. All 3 iPods played fine in our Bose SoundDock. All 3 iPods connected to our PC and iTunes as well.
The only combination that didn't play - was the 1G Touch in the MINI. I figured that there must have been a problem with its dock connector / and or the adapter cable. I planend to bring the 1G Touch to the Genius bar for evaluation. Having been to the Genius bar before, I knew they would ask me what troubleshooting steps I performed and if I attempted a restore. So, I restored and the problem went away. Now when I connect the 1G Touch to the MINI adapter, the "Checking CD" messages displays for approx 10 - 15 secs (which is a little longer than before), but then everything plays fine.
The only thing about the 1G Touch that changed between its working and non-working states were the adds and deletes of Apps that I perform almost daily. I can't imagine how any App that didn't exhibit any bugs could cause this problem, but it is really the only explanation I can come up with.
I doubt that these symptoms will be the same as anyone else might be experiencing, but the bottom line is that sometimes Restore is the way to go. Hope it helps.