This happened on both of my multisite Wordpress installations. I installed the Gantry 4.0 update at the network level when prompted. Thankfully all of my frontends and most of my backends remain intact, but every blog that uses a RocketTheme has had the Gantry area rendered completely useless. Tabs are gone, and all the settings appear on one page, on top of one another. Check out the attached screenshot.
This same exact thing happened to me. The Gantry backend is completely useless now. I doubt you're the only one affected, and I'm positive you'll never get an answer. Really these forums are mostly useless.
Well, to be fair, I think it's hit or miss depending on the subforum - in some of the Wordpress theme subforums I get great attention. Wordpress plugin subforums are pretty bad.
I'm tempted to go post in the Gantry Google group, but we'll see. Obviously nobody is watching THIS forum, and I feel like this should be a pretty important one for them.
Here's how I fixed MY similar problem (watch how fast they come NOW, to tell you how bad my solution is, lol)
The problem in my case, and probably yours, too, is that the newer Gantry is completely incompatible with the older Gantry theme I was running. So here's what you do:
If the problem had persisted much longer, I would have definitely reverted to an older version of the plugin. However, just today I noticed an updated version of Gantry, 4.04, and installed it. It seems to have fixed the problem!
That'll teach me to install major updates right away.
Yeah it's totally "updater beware" when dealing with any content management system, and it's just unfortunate that Wordpress doesn't seem to have a slick backup system like Akeeba. I have been trying out a new backup plugin that seems to be a great way to go so far, but I haven't actually had to backup anything from it yet, so I can't really recommended it 100% yet.
If you want to check it out it's called WPB2D (Wordpress Backup to Dropbox). You set a schedule and it automatically and regularly backs up your entire website and database to your Dropbox account.
wpb2d.com/
I had the exact same problem using a rocketlauncher for the Ximenia theme, with the latest version of WP.
To solve, I deactivated the gantry framework, deleted it with all files, reuploaded the 4.0.4 version fresh from the gantry site, activated the plugin and now it works great.
I did all this from the WP admin dashboard, BTW.
Site data and layout seems intact, so I don't see any downsides to this approach.