I've got a Ford Edge with Microsoft's Sync system. It works pretty well with both my iPhone and my 5th Gen iPod. Playlists and all.
The biggest issue I have now is that the play count on podcasts (and presumably all music) doesn't get updated/credited for items played via Sync. This is an issue for me since the iPhone's relatively small storage space makes use of Smart Playlists essential, and most of my playlists have "play count - 0" on them to ensure fresh podcasts are synced up. I'll have to post about that in a new thread perhaps.
re: your specific issue, I don't think this will fix it, but Microsoft's Ford Sync is very picky about all metadata tags being complete on all items (artist, track, album, etc). Sync won't index items that don't have proper metadata, and if it doesn't index them, I'm going to assume it can't see them to play them under all the right circumstances.