OK so this is a little weird.
First, when I install WPMU Dashboard it wouldn't let me access the plugins page. Every time I clicked on the plugin link it redirected me to the WPMU Dashboard page. It's not doing this any more, so is it not supposed to do this? I'm guessing not since the WPMU Dashboard doesn't list any of the other plugins that are loaded.
Anyway, because I couldn't see any of my other plugins to activate them, I went to the WPMU dashboard and deactivated it. This was bad. The Dashboard was removed from the menu, but the Plugins link still redirected to that page. This caused me to keep getting a "You do not have access" error.
I played around trying to figure out what the problem was. I checked the database and wpmudev-update or whatever had been removed from the list of installed plugins. I also found what I believe is an error in
update-notifications.php line 146. The code reads
register_activation_hook( __FILE__, array( $this, 'deactivate_plugin' ) );
I'm guessing it should be
register_deactivation_hook( __FILE__, array( $this, 'deactivate_plugin' ) );
So tried to update the database based on what was supposed to happen in that function, but still no love. Fortunately, I had WP Smush Pro installed and when I went to that page, the notification bar was up and I was able to reactivate the Dashboard. However, it was still not letting me go to the plugins page. So I deactivated the Dashboard again hoping the new code would fix the problem. It didn't. Redirect kept happening.
Finally I just deleted the wpmudev-update folder, and now the plugins page loads and says the Dashboard has been deactivated because the file doesn't exist. I'm guessing this means you guys hook into the plugin activation/deactivation/run plugin sequence, and something goes wrong in there since the plugin should have already been deactivated. Possibly the local projects transient? But you know your code better than I do.
Anyway, it's great that it's working but I still want to know what the problem is. So I reactivate the Dashboard and now I can't get the problem to repeat. The Dashboard is on and works, but I also have access to the regular plugins page. Also, I checked the database and the only redirect option that exists is for WP Smush Pro.
So I don't know what happened or why. The only reason I'm sending this is because I thought you might want to fix what looks like possibly a code error and/or try to test this out on your own and see if you can recreate and fix whatever happened the first time. For reference, while I have the files for several other plugins uploaded, WP Smush and WPMU Dashboard are the only two that have ever been activated. Also this is a fresh WP install v 4.6.1.