Ok, so i think i can now see the issue. It looks like you need to move all the files/folders you want to sync into the sub-folder created when you set up the sync. I think by default it is set to a folder called "media cloud store".
Even though it syncs the folders when you put them in the parent directory, it won't sync the files within, so it seems to be a weird issue with recursively looking through each folder. However, the fix for me was moving all of my media, complete with my original directory structure, into the sub-folder.
Of course, you do then need to relink all your media bins within projects, but that should only take a few seconds and be mostly automated when you open up a project and select relink.
It's not very well explained and quite unclear, but that did resolve it for me. Pun intended