I have a couple of sites which use Jetpack's mobile theme, since the regular theme is not responsive. On those sites, I just noticed that after clearing the cache, if the first visit to the site is made on a mobile device, the plugin will cache the mobile theme's design. If someone visits the site on a desktop computer after that, the plugin will show the mobile theme (even though it should display the regular theme), unless I manually clear the cache.
As a suggestion, maybe you can implement some sort of check in the code so that the plugin knows when to display the mobile theme and when to display the regular one.
I thought I'd mention this so you could take a look. Maybe others are having this issue too. BTW, thanks for such a great plugin.