WP-Touch plugin more issues

Hello

I have another issue with this plugin. First I like to say it works beautifully on how easy it is to use and I am using the free version but my other issue is the following:

my employer uses a custom theme into WordPress to meet its branding, but the WP Touch plugin can’t seem to grab information from its WordPress pages, it does but it cannot grab information with those pages that utilizes php template files with WP Tags inside the custom page.

Is there a code I can include inside my PHP files for WP Touch to grab the information? or can I make changes into the Pro Version that would resolve this issue and if so, how? I need to make the case in buying the Pro version with my employer on how this could (can) be resolved using the Pro Version.

Thanks!