I have this problem, but also tunes appearing on the phone but not in MM, and I can't see them with iTunes either.
I used MM to delete everything on the phone, and now MM says the phone is empty, but I still have 1500 tracks on the phone that play just fine.

iPhone 4, IOS 7.1.2
MM 4.1.6.1736, ("current version" when I check for updates)

Are these supposed to play well together?

Which version of MediaMonkey was used to sync them?

Used MM to put a bunch of music on my Iphone 6+. Only a little of it is visible in the Iphone -- it all appears in MM as though it were on the Iphone... -- I hate Apple...but, I'm stuck with it. Any idea what the problem is?