As mentioned in the help section of SmartPlaylist, you should quit SmartPlaylist before syncing your device.
With the new iOS 4, "to quit" means to really shut it down, not just hide it in the background (new "multitasking" ...).
1. Press your home button to close/hide SmartPlaylist
2. Double-tapp the home button
3. Press your finger on the SmartPlaylist icon in the bottom, until the "Quit"-badge appears
4. Tapp on the "Quit"-badge
--> Now it is really closed.