Just a follow up to this in case anyone has the same issue.

Disabling other plugins didn’t work – any time I updated to a newer version of WP-Filebase Pro it would wipe out the Remote Sync settings.

The solution was to download, install and activate the new Dropbox WP-Filebase extension *before* upgrading to the new version.

With the dropbox extension in place first it worked perfectly.

Thanks Fabian!