One of the drawbacks of how WordPress handles shortcode (and post type/field) registration is that it happens anew every time a page on your site is loaded.
When WPtouch handles a mobile request it uses its own mobile themes to handle the display of your content, so when a visitor to your site access it with their smartphone, your desktop theme is not loaded.
If the code for your shortcodes, etc. is inside your desktop theme, whether directly or through a framework inside it, they don’t get registered when WPtouch’s theme is loaded. And, of course, because WordPress then has no idea they exist, WPtouch can’t display their output.
We’ve been able to work around this for custom post type support –?short of trying to load your desktop theme’s functions.php (and subsequent included files), though, there is little WPtouch can do to load shortcodes registered by your desktop theme.
For these features to reliably work for your mobile site, theme developers will need to either move things like this out of their theme files and into a plugin or, in the alternative, ship a basic plugin that just loads the necessary theme files and calls the limited code required to activate those features for mobile requests.
We have example code for such a helper plugin available for review – I would welcome theme/framework developers to collaborate with us to ensure that the features their customers rely on work seamlessly across both desktop and mobile themes.