I'm pretty sure I'm having the same problem here.
It seems that with the advent of Apple Music and the iCloud Library, the model has shifted from your Library being based on a computer and being pushed (synced) to portable devices, to the Library being based in the cloud itself (i.e. that's where the "official" or "original" copy of music/playlist/etc. data is kept), from whence it is pushed (synced) to all your devices, whether they're stationary computers, or portables.
I have two iPhones (recently upgraded to 6 and haven't disposed of my old 5 yet), and two computers (iMac and Macbook Air), so what I say here is the best explanation I could come up with to describe the behavior I witnessed coming across this bug. Hopefully some Apple engineer will read this, and maybe it'll help. My ability to actually tell what is going on, however, is severely hampered by not having direct access (a web portal maybe?) to the iCloud Library itself, only the mirrors of it on my devices (which are flawed and evidently do not update very quickly).
I can't speak for the first device I activated (my iPhone 6) because there was no other platform to see if it was syncing with. When I updated and activated Apple Music and the iCloud Library on the others though, it seemed as if there was a brief period (on the order of half an hour) during which changes were synced properly, including playlists, ratings, play counts, and song removals (I'll get to additions later). After this period ended--I cannot say definitively what ended it but I suspect it has to do with expiring/terminated connections), absolutely no more changes were synced at all, with the sole exception of music library additions. Moreover, any changes I made on my iTunes were actually reverted seconds later--I would try to delete a playlist and it would pop back up before my eyes.
The basic problem to me seems to be related to devices pushing updates back to iCloud's Library. For some reason devices are suddenly and irreversibly losing their ability to push Library changes back to iCloud. The only exception is adding songs, which I suspect is because the actual change is performed within Apple's servers (your device submits the addition request to Apple Music, which then passes it to iCloud Library), while things like modifying playlists and deleting songs must go directly from your device to the cloud.
That's my best guess. I have a decent knowledge of programming and networking and such, but I'm by no means an expect. All I know is that if this crap doesn't get ironed out, I'm going to have to take a look at Spotify.