That is helpful information. The indexer is probably crashing on one of your files - the question is which one. The problem file lies at the end of the J's or the beginning of the K's.
Now, clarify, is that songs starting with A-J or albums starting with A-J? It will be easier to track down if it was albums, assuming the files are organized in folders by albums - copy the albums starting with J and find the first one that isn't complete. If they are all ok copy the K's.
If it was files, do a find on your PC of all songs then sort by name, then copy the J's over into a folder on your Pre. If it gets them all, the problem starts in the K's. If not, look for the first one that doesn't copy.
Once you've identified the song or album crashing the indexer, you can try to figure out what it doesn't like, or just skip that file (or delete it from your phone). If you have the CD, try re-ripping it.
I don't know if the indexer does both music and pics at the same time, but if so, the problem could be with one of the album art images in the music folders. If you have only embedded images (no separate image files) that is probably not the issue.