Is there an issue when both applications are running because I keep getting multiple error alerts regarding conflicts in Dropbox. The iPad addition also keeps saving work in a dedicated conflicts folder. I have the iPad saving in Dropbox/Apps/Scrivener.
To add to that, I had a Scriv project open on both iPad and MacBook at the same time, but before moving from working on one to the other I made sure sync was complete. The iPad had gone to sleep in the meantime, when I woke it up it asked me whether I wanted to sync. I did, and it worked beautifully