I have over 12,000 tracks on mine from two sources and have not had any issues with it scanning the files. I have transferred my iTunes Library music to a 128GB card and have copied about 500 High Resolution FLAC and DSD files to the internal memory. I have a Mac and used Dapper to transfer the tracks. The scan is limited to 10,000 tracks and take about 30 minutes. Can you browse and play your tracks using the folder view? The UI is not a refined product, but is just a bit sluggish with a lot of tracks. If the files are on the Jr. and can be played, the problem is most likely with the file tags. If the files can't be browsed and played, the problem is most likely with your connection to the PC. Try just copying some directly to the SD card to see if they will scan.
Good luck.