Mobile Version Difficulties

I have a custom slideshow that I use on most of my sites. I create a div with an ID, and I have a a JavaScript that looks for that div by its ID, and if it is found, replaces the contents of the div with the slideshow. Otherwise the div has a message that says you must have JavaScript enabled to see the slideshow. The slideshow also detects when it is being viewed on a mobile platform and switches from a Flash presentation to a scaled back HTML/CSS/JavaScript presentation. It all works great, and I use it a lot.

On Gavick templates though, I am having difficulty. It works great on Gavick when in Desktop mode. The slideshow detects that it is on a mobile and displays correctly.

But whenever I switch to the Gavick mobile desktop, the div is no longer replaced by the slideshow, and it just displays the message that you must have JavaScript enabled.

I am not understanding what is going on here. As far as I can see, the only reasons that the message will display is if JavaScript is not enabled or the JavaScript cannot find the named div for some reason.

Any Idea what is going on here?

I set firefox up as a mobile device so I could see what was happening, and it looks like the mobile version is stripping out the Javascript that I use. In, fact, it looks like it is stripping out more than just the JS. Is there any way to allow javascript selectively? Is there a description somewhere of what the mobile version does and how it works?