I'm really confused now. It seems to not work intermittently, despite nothing changing.

I'm not sure why it was trying to include the /snap directories, they weren't part of my selection. I'm also still not sure why it worked when I manually ran the backup, but not when run from the schedule, but I think I have resolved the issue. In the "Skip folders" selection, I should have put snap, not /snap. It seems to be working now.