I have the exact same issue. The Start/Stop Time is overlooked after every sync in MMA. Here is something I did run across, if you have bookmarking enabled, it will start where it left off. It should be possible via SQLite query to update the bookmark time to the Start Time, I just need to know what ...

I have a Galaxy S3, Verizon Stock 4.1.2. MM 1.0.4.0168. I was flying today and had to turn off my phone to fly. I have restarted it a couple of times the last few days, but I did one thing different, I put my phone into Airplane Mode and turned it off. Turned it on and suddenly all of my Playlists ...