Well, it depends, what do you have the tag priority set as in Rockbox? ID3v1 then 2, or 2 then 1?
As for not updating completely, if you didn't wait long enough before restarting that's possible. If you had embedded album art that can also cause an incomplete update. AAC files being present can also break an update.
As for limits, it seems to be 10,000 songs.