CASE: IPhone 4S, iOS 5.0.1, not possibile to syncronize tracks (only a few). Others appearing in gray, but not active. I worked on that for 4 hours, cannot tell you angry i was.
So, this is how it WILL work.
1. Open itunes - click on your device when recognized
2. Go to Summary - check "manually manage music and videos" - apply
3. Go to Music - under your recognized device. Now you can select and DELETE all of your tracks from your device. Do it. Delete them all as long as you have a back up somewhere (in your library).
4. At the bottom of section "music" you will see "Autofill from" - chose the most reliable source (I used the folder "music" under Library). In case you dont see "autofill form", just open the page in a new tab (righ click on "music" - new tab)
5. Press "autofill". You will see your tracks comming back to life. In case you have "tones" with the same problem simply "drag and drop" them on your recognized device.
I hope these will help you, too.