Mobile theme plugins typically sniff the user agent and just switch out your main theme for a bundled “mobile friendly” generic one. In the process, any shortcodes registered in your theme are no longer recognised, and they just display as plain text.
Check out the plugin documentation, or contact the developer, and see if they can offer any insight. I would also check out the source of the plugin and see what actions/hooks are available – there will (almost) always be some way of “injecting” your original theme’s functionality back into the plugin theme.
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