I tried to upgrade Quick Submit and Custom Header plugins, unfortunately there are not found in the installed plugin tab, then in the plugin gallery they show that can be upgraded. When I click to upgrade it does not upgrade and gives a message Plugin already installed and is newer than the version available in the gallery
With this message it takes back to the installed plugins with no plugin available there.
For the Quick Submit plugin you should be able to access it under Tools (on the side menu) - do you see it there? Quick Submit is a bit different as it accessed through the import tools, unlike many of the other plugins.
For the custom header, what version does your plugin gallery show as you having installed?
I have the same problem as you with the bootstrap3 update. it tells me it can be updated, I click on it and it gives me the same message as you. I actually already have the latest version installed. so I assume it’s a bug in the new version