Updating icloud music library without messing up playlists

I am trying to upload my music to the iCloud music library, when i try to do this it removes lots of songs from my playlists. I can restore these without issue with backups of iTunes Library.itl .

I have tried resetting my iCloud library but get the same issue.

I used iTunes match a few years ago without to many problems. I'm now using a different desktop and signed up for the service again. I think this probably has something to do with the issues i'm facing.

I'm happy to delete/reset the iCloud music library and start again, if needs be, but the best solution would be to add the new music i have and update playlists.

Can anyone help?

Thanks in Advance.