ITunes stuck on "Waiting for changes to be applied"

Here are the symptoms I'm seeing:
- If I restore my phone, or delete/reinstall iTunes, or uncheck "Sync Music", wait for a sync to complete, recheck "Sync Music", ONE sync attempt will complete. I try adding one additional song and re-syncing the device, it gets stuck.
- If a sync doesn't complete, it gets stuck on "Waiting for items to copy" or "Waiting for changes to be applied". Via fs_usage, it seems like nothing is happening during this phase. I've left it for two hours and it doesn't move on from this phase unless you manually cancel the sync.
- It's manifested itself on two different phones - an iPhone 4S and a iPhone 6.
- Each phone has enough space for the items I'm syncing
- Sometimes iTunes or gets confused and moves the entire music library on my phone into "Other". Recently I had 42GB of "Other" on a 55GB device. See attached screenshot: http://monosnap.com/file/AaDzqWpgtNXtfTYdy8iscfTKrkZGWC
- The problem has persisted across multiple versions of iTunes (at least versions 11 and 12)
Here are the things I've tried to solve the problem:
- Restore the device - as mentioned, works one time, further syncs fail
- Turn my laptop off and on
- Turn my phone off and on
- Replace "iTunes Library.xml" by moving it to the Desktop and rebuilding the file (really fun as I lost all playlists, import date info and most played information by doing this)
- uncheck Sync Music and recheck it - as mentioned above, this works one time, this method is also error prone (takes 3 or 4 canceled syncs before it decides to actually transfer the songs)
- signed out of Apple Store
- repair disk permissions
- repair disk
- trace iTunes process with fs_usage, will try dtruss next
- remove the SyncServices/Local directory - didn't do anything
- remove iTunes and every trace of it I could find (com.apple.itunes and related plist files) and reinstall from the Internet - I got one good sync after this and then it got stuck again.
I would appreciate your help as I'm at wit's end here. If there are any debugging logs or further information I can post, please tell me - I'm a software engineer by trade and have a fairly good idea of how to operate a machine (though not really how to debug a closed-source binary, maybe I should learn how).
Thanks,
Kevin

This problem started last year when ios 8 was released. I think apple is trying to force users to buy music on iTunes store and that's why it's impossible to sync other music and also that's the reason why they haven't solved this serious problem. That's really disappoints me and i'm angry with apple because i have like 10 gb of music in mp3 and i can't sync music from iTunes to my iPhone.

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1) Plug your iPhone in to iTunes.
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'File' > 'Devices' > 'Transfer purchases from "_______ iPhone"
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----CONTINUE READING IF THIS DOESN'T WORK----
9) Click 'Restore iPhone'
10) Let iPhone restore (could take 20 minutes)
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----OTHER THINGS TO CHECK BEFORE YOU RESTORE----
1) Is your iPhone running the latest software version?
2) Is your iTunes running the latest software version?
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-----OTHER THINGS YOU COULD DO-----
1) Re-install iTunes (could work - probably won't but you can give it a try)
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3) Re-start your phone by holding the 'Home/Touch ID' button and the lock button at the same time and hold until the Apple logo appears.
----NOTES-----
Since updating to iOS 8 and iTunes 12 I haven't had this problem. You might want to update to iOS 8.1 and iTunes 12 - this could solve the problem too.
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After several nights of leaving it connected all night I would find that the songs had physically copied and were occupying the ~45 gb of space on my iPod's storage, but were not showing up on my local library, instead listed as "Other" in iTunes and otherwise unusuable, or they would show up, but I'd have ~45 gigs of "Other," 45 gigs of "Audio," and would be "Over Capacity," by 30 gigs or so. OR it would be "Waiting for Changes to be Applied," for 12+ hours.
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This for me was successful as a workaround, but this is not a solution. Apple needs to fix this crap. Maybe they just want to make it so difficult to have a physical library of music on the local storage of the iPod that we will just give up and sign up for their Match service.

ALSO, on the iPod under Settings>General>iTunes Sync, you may need to back out of the "iTunes Wi-fi Sync," and reopen it to get it to update.
(I use iTunes 11.1.5.5)

ITunes stuck on "Waiting for changes to be applied"

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