I had the same problem with my 3GS after an iOS5 update and found the following link helpful: I found deleting the music and re-syncing solved the problem (at least for now!).
2) Under your devices music tab, de-select -> Click on Sync (this should remove your itunes library from your iDevice
3) After completing step 2, go back to the music tab and re-select Sync Music -> then click on Sync
4) After completing step 3 your iTunes library should have returned to your iDevice
As I only tick the music I want to load individually, I deselected everything, selected synchronize iPhone, then ticked the boxes I wanted to load again and synchronized a second time. Worked immediately.