I've noticed similar with my phone (not jailbroken) also - I've noticed that if I amend any of my iTunes track's details (e.g. artist, album etc) then when I resync with the phone, it moves across a NEW copy and removes the detail of the old from the iphone music list .. but I suspect it's not deleting the original file.
that's my experience anyway and if anyone has a fix for this (bar restoring the iphone to factory default) then please let me know