Had the same problem at first. When sync itunes to new iphone 6 plus, most of the songs in my music library synced, but not all of them. The ones that didn't sync still showed up on the phone but they won't play (like "ghost" songs), instead skipping to the next song. This occurred on brand new phone 6 plus that I bought on 10/28/14, and used latest versions of iTunes and iOS 8.1 to sync.
I've read a lot (you find more searching on google) and there are over a MILLION online posts about this problem, but no consistent fix yet.
One thing I've noticed is a discrepancy between the total number of "items" in my iTunes library, and the total number of "songs" that get synced on the iphone 6 plus.
My iTunes library has over 2626 "items" (to see your total, click on Library>Music>Songs, and scroll to the bottom of the list it will tell you the total number of items in your library)
However, after I sync, the iphone 6 plus thinks there are only a total of 2515 "songs" (to see your total, turn on your phone and click on Music>Songs, and scroll to bottom of list to see the total number of "Songs"). The iphone seems to be counting the combined total of both the grayed out songs, and the non-grayed out songs - regardless of whether they play or not
The source of the problem seems to be in the current version of iTunes software. While my phone is synced to iTunes (and still plugged in by USB cord), the iTunes software correctly lists my phone under "Devices" on the left hand side. If you click on the device listed, and then click on "Music" at the top of the iTunes banner (choices: Summary-Info-Apps-Music-Movies-TV Shows-Photos), you get to a mostly blank white page titled "SYNC MUSIC" with a check box next to it, and next to this it lists the number of "songs" to be synced. In my case, for some reason this is only 2515 songs, and not the actual number of "2626 items".
This seems to be an important clue to the source of this common problem
Many of the online suggestions by other users with this problem find that a common temporary fix that sometimes works is to check and uncheck the box on the "SYNC MUSIC" page (listing the incomplete total number of items in the library) and then re-sycn. This DID work for me !!! But other users warn it's only a temporary fix, and the problem reverts if you try to sync your phone again. So once you get all your "items" on the iphone this way, they suggest avoiding any further syncing until Apple fixes the problem
The fact that unclicking & reclicking "Sync Music" works (under "Music" when clicking on the listing for your device in iTunes) suggests this feature in iTunes is part of the source of the problem. Apparently, Apple's iTunes Sync software sometimes only syncs "ITEMS" that Apple recognizes as "SONGS" !!!
Yet many of my other "items" are in fact songs, but many without attached artwork, or artists, or albums. Many are older versions of songs not currently for sale in iTunes online database, or classic songs in older albums no longer available. Some of my "items" are video recordings of college lectures etc...which are treated like songs in my iTunes library but won't sync to the iphone 6 plus.
Interestingly, my iTunes library plays all of these "items" just fine. Also, it still syncs to my older ipods just fine, including all the "items".
The only problem seems to be with syncing to the iphone 6.
HOPE THAT APPLE TECHS READ THIS AND CORRECT THE PROBLEM SOON IN THE NEXT ITUNES