I have had similar issues, and eventually ended up disabling iTunes Match, and doing a hard sync via USB cable with various iTunes settings detailed in the last couple of comments here:
https://discussions.apple.com/thread/5414221
The Users Manual on p. 63 discusses iTunes Match:
http://manuals.info.apple.com/MANUALS/1000/MA1565/en_US/iphone_user_guide.pdf
-- "Turning on iTunes Match removes synced music from iPhone."
-- When iTunes Match is on, downloaded music is automatically removed from iPhone as space is needed, starting with the oldest and least-played songs. An iCloud icon ( ) appears next to removed songs and albums, showing that the songs and albums are still available through iCloud but not stored locally on iPhone."
As I replied to Steve in the thread below, I am not sure what the effect of turning iTunes Match back on will be, and am looking forward to an expert's feedback. In other threads, it was recommended to do a hard reset of the new phone in iTunes, and then re-sync all. TBD.
https://discussions.apple.com/thread/5393520?answerId=23298699022#23298699022
The Users Manual quotes above seem clear, though, that iTunes Match was designed intentionally to remove local song files on the phone. Bummer IMO.
Good luck!