Hi All,
I have the same issues as most of the users here.
I have a 128 GB iPhone 6 and I am using the latest iTunes 12 for Windows with around 85 GB for 15,000+ songs that I have purchased over the last 25 years, so a huge music fan here. I went for the bigger iPhone becuause it has enough storage to sync the whole library (so no need to carry around my iPod Classic when I want it all). I also have iTunes Match (which I am thinking of dumping at the next re-subscription date - but that's a different matter).
At first, I noticed that all songs apart from the ones purchased in the iTunes store were copied over via sync. I could not get to sync the purchased ones at all. Then I noticed this little post about duplicates: http://robservatory.com/a-nasty-little-itunesios-bug-may-be-causing-media-sync-i ssues/
I found one album which had 14 of its 28 songs duplicated. However, when I listened to them, they were completely different songs, but cut to the length of the original album songs. Something must have gone wrong in the past, since I always backup my iTunes library locally every now and then, and the old one had these duplicates as well. After I removed them, the sync went well once with ALL songs. By then, I had already restored my device several times.
So, let's make this clear: Yesterday, before I decided to transfer the new Foo Fighters album to iTunes that I had bought on Tuesday, I had all my 15,000+ songs on my iPhone - and I was happy... and scared to sync so that I would have the new FF album on the phone. But I just can"t leave this album unsynced - I have to listen to it... it's the new Foo Fighters album, after all! ;-)
Turns out my reservations towards the sync were right.
Tried to sync. Took ages in 'Waiting for the changes to apply'. Cancelled sync. Lost a few songs including album art on the phone. Tried to delete all music on the phone through 'General -> Usage'. Did not work. Un-checking 'sync music' would leave orphaned songs that come up as 10GB of 'other'.
So I backed up the phone yesterday and restored it for the n-th time over night, hoping it would work and transfer everything from scratch. Woke up this morning finding the phone had not synced. Tried to sync at least the FF album. Took ages. Stopped the sync, un-checked music to be synced, applied, changed it back to only sync the FF album, and then it worked within seconds.
I must have tried every single solution people came up with, but this seems to be an iTunes, iOS or iPhone issue that Apple will have to fix.
I think I will try once more to copy EVERYTHING over, then never sync again until Apple finds a fix.
It's really upsetting given the fact that a lot of people who bought the 128 GB model chose it for exactly these reasons: to be able to sync their whole lotta music and have it with them all the time.
I really hope Apple will publish a fix soon. They are not doing themselves any favours here.