Why is my iPhone skipping all of my music?

Any time that I make a change in iTunes on my MacBook and 'apply changes' to my iPhone 6, I end up having to re-sync the whole music library. Each time I try to play my music it skips through all of my songs that haven't been purchased directly from iTunes. It will only play songs that have been purchased from iTunes using my Apple ID. Once I re-sync the music, it's fine. This seems like a lot of unnecessary synchronizing, though.

Is there a setting that I should change, or is this simply a bug with iOS 8 or iTunes 12.0.1.26?

iPhone 6, iOS 8.1, Mac OSX Yosemite, iTunes 12.0.1.26

Most likely, the music files on your phone have become corrupted. I suggest you connect you iPhone to iTunes, and go to the Music tab of your iPhone. Uncheck the box at the top that says "Sync Music" and click "Sync" to remove all music files. Then check the "Sync Music" and sync again. If that doesn't work, go to you setting and erase your iPhone and start over. And if THAT doesn't work, restore you iPhone.

What type of changes are you making in iTunes? Where do you see the words "apply changes to the iPhone"?