I cannot sync songs from iTunes(12.3) to my phone. I tried to copy manually even that didn't work out. They are not copying at all. Even the books from iTunes copied after 2-3 syncs in each sync some books. Seems like a serious issue here.
iOS is 9.0.2(jailbroken)
I have this problem too. About 2 weeks ago I put my jb iphone into a boot loop, so i had to restore it to 9.1 then downgrade it to 9.0.2, thats when i think the itunes quit syncing my music. I dont think it is the jailbreak itself but the downgrading process. So i attempted another DFU restore and went to 9.1 and then i started syncing a bunch of my music on 9.1 which it worked fine then I downgraded to 9.0.2 and then the syncing started screwing up again. So I then jailbroke my phone from there. I do have synced music on my phone, but i cant add any more music and all my purchased music will not download to my phone. So thats where im at with my phone.
Did you downgrade your phone from 9.1 to 9.02.?
I did find a little information on the Reddit forum on a fix, but that includes ifile and deleting some files from itunes folder in your phone. I didnt want to do all that so I just downloaded google play and I listen to my music library from there.