My guess (and just a guess), is that you either a) crossed some overall file size limit... Not sure why that would make a difference but if initially you had 2GB of music and then you had 8GB, maybe it's choking after the 4GB point or something.
Other thought is that one of the files you put on there is specifically choking it... Either something in the filename or the metadata etc is causing the running android auto software to fail midway through processing all the files and that causes some to not show up.
Try again, with just the original first working batch and make sure that works, then try adding half of the new batch to see if that works, if it does, add half the remainder, and so on and so forth til you find the problem file or limit.