I've found that if you're not logged into the WPMU Dev dashboard on individual websites then updates will appear in the ManageWP dashboard but you can't update them from the ManageWP site. This occurs on any website.
I reproduced this by trying to update several WPMU plugins from the WPMU Dev dashboard to hummingbird but they wouldn't update. I logged into the WP admin website and found that I was not logged into the dashboard. Once I logged in I could update the plugin both from ManageWP and the WP dashboard.
The biggest problem is the dashboard just keeps logging me out on a periodic basis. Problem #2 is that even though I have the option checked to do updates automatically it also doesn't update if you aren't logged in. So I'm left with having to log into each one of my many sites to log into the dashboard just to update a plugin that should automatically update. If that were to fail it would be nice to be able to do it from the ManageWP dashboard. That's the point of the system, centrally manage all sites from one dashboard. WPMU Dev is costing me lots of time.