This only happens with some plugins, after starting the synchronization some plugins are not reported as updateable even if in fact they are.
Plugins sometimes don’t show up in WordPress (ie as an update notification in the admin bar), until I specifically click on “Plugins”, which probably starts an internal process where WordPress checks for any available updates. Only after the update available does it show up in WordPress, and also in MainWP when I sync again.
Maybe MainWP could automate that “manual visit to the plugin page”? And maybe show if there are plugin notifications in the backend? Would be great.