Experiencing a similar issue here.
Ringtones will not seem to transfer to my iPhone 4 (upgraded to iOS5) via iTunes 10.5.
Selecting the iPhone under Devices in iTunes shows no Ringtone category in the top middle section. There is no Ringtones category to check and uncheck.
If I drag a .m4r type ringtone (32 seconds long) onto my iPhone icon in iTunes, it transfers but shows the file in gray. Syncing at that point does not make a difference.
The custom ringtones I drag to my iPhone do not appear in the Sounds preferences, only the factory ringtones appear.
I've tried creating new .m4r ringtone files, restoring the iPhone twice (second time as new iPhone), un-installing iTunes 10.5 and all related .plist files, but no luck.
I am thinking of doing a complete reset of the phone and trying it on another Mac. What do you think?