I have exactly this issue also. Tried multiple attempts to re-add iCloud music to my photo (via settings -> Music -> iCloud Music toggle - choosing both merge and replace) and no luck. Is everyone seeing this? Has apple acknowledged it?
When I delete everything and toggle the iCloud library off and on again and choose replace it would work, but i just made 25 GB of songs offline available and I will not do this again. Also: My albums that I can't sync with apple music but upload manually don't show up either. I hope there is a workaround.
I decided that since Apple music had almost everything in my library I would just replace everything with the apple music stuff (after thoroughly backing up my library) and then I downloaded everything again. But no after this I still can't get my mac to sync stuff to my iPhone.