FID 100 is the root playlist. Apparently, it contains more than 133 entries ( a mix of playlists and tunes). You can check by connecting to your empeg using FTP and looking at the file /drive0/fids/101 or /drive1/fids/101. The length field in that text file tells you how many entries it has. Do you have more than 133 different artists? Given the size of your drives that is a possibility. I have more than 133 artists, but I have them subdivided by genre... you can also verify that with Emplode.

You didnt verify to me that the countup of tunes in EMSC is still at zero when you see the terminal output you posted, and then starts going to circa 2500.