The same thing is happening to me... I was a previous iTunes Match subscriber, so I have reset my library to a previous version and followed Apple's instructions to reset (delete) my iCloud Music Library as described in this article (If your music library shows incorrect details with iTunes Match or Apple Music, and you previously cancelled an iTunes M…).
However when I restore my library from an existing backup and try the process again with the new reset library, the same thing happens again. Songs just disappear from playlists (I think it's songs that haven't been matched to the Apple Music library successfully.
I note, no songs are deleted from my library, just missing from playlists (which I've taken a lot of time to organise), and songs that seem to be removed from playlists have a "Removed from iCloud" symbol on them.
Only a small portion of my library actually uploads to iCloud Music, and the playlists are not fixed when the iCloud Music Library is finished syncing.
I'm on Mac 10.10.4 (I know this is a windows forum, but it's the only place I can find this topic), and also use an iPhone 6 and Windows 7 computer.
Any help would be appreciated, this is very frustrating!