It's pretty well known that RocketTheme's Gantry plugin doesn't play nice with JetPack, and I know it's not your fault. That darn spin.js error breaks things like the widget page, where you can't drop down the widget areas, for example.
Anyway, on my multisite installation, I find myself disabling JetPack from the network level regularly for a few minutes to mess around with widgets, for example, and then reactivating it. Lately, however, I've noticed some strange behavior: once reactivated, JetPack is automatically "connected" for all two dozen blogs on my network EXCEPT for the primary blog. Each time, I have to go into that primary blog and manually reconnect JetPack to WordPress. I have no idea why, and perhaps this isn't your problem since I shouldn't be constantly activating and deactivating it anyway, but I thought I'd let you all know.
Thanks for a great plugin! Would still love to see IntenseDebate make an appearance. :)