Manually managing music on Ipod Touch

I have a second generation Ipod Touch with the most current software and the latest iTunes software. I also have more music than will fit on my Ipod Touch. So... I have set up multiple smart lists for my Ipod...like 70's music, 80's, my favorites...etc. These are seperate from the smart lists I use within my entire music library to help sort it. Ok, so when I plug in my Ipod Touch these smart lists show up within the Ipod Device menu on the left. I the click on the Music icon below where my iPod Device is shown and have my settings at 1. Replace all items when filling, 2. Choose items randomly, 3. Choose higher ratings more often, and finally reserve space for disk use at 4 GB. I use the extra disk space for podcasts, pictures, movies...etc. I hit AutoFill and boom...I have tons of music put onto the Ipod all sorted...great. Well after the recent Itunes update and Ipod update, the next time I sync my Ipod a random amount of music is just deleted from my Ipod. Still on my computer but not my Ipod. Like I just had 2GB of songs taken off when I synced it....leaving me with 7.4GB of free space.

This never happened before. I would even put podcasts and movies until I was almost out of space and songs were never randomly deleted. I reset my Ipod and still have the vanishing music. Any ideas?