Why wouldn't they update the NAV?
Because the NAV system for 2011 doesn't get updates as often.
For 2011 if you bought nav, you get a few of the Sync features (voice communication with the car) but you get your navigation, traffic, and business search through the nav company, not Ford. Because of this, you don't get access to any of the Ford "Traffic, Directions, Information" features that are part of the Sync package. They carved out some of the Ford Sync functionality, and stuck the third party nav package in it's place. So this requires a separate update from the normal "full" Sync "TDI" package.
For 2012 models, Ford did it right, and now even nav owners get the full Ford Sync "TDI" services, meaning everyone gets the same updates.
But for the last 10 months my car has been stuck at v3.1 despite them announcing new Sync updates.
Both 3.1 and 4.0.2 will be updated. Ford specifically mentioned the 2011 and 2012 Mustangs in the press release. Check out Autoblog if you want to read the press release.
But there's no update. They claimed they shipped it today, and the version number they listed was released months ago. Maybe they mean they're shipping that old version for the cars that haven't received it yet? Nonetheless that would mean it's not a *new* update.
Also, they explicitly said "select 2011 and 2012 models". Where do you see mention of 3.1 being updated?