Hi,
My best guess would be something like an extra closing tag or a missing closing tag on an element in your custom feature.
The way I would troubleshoot the problem is to use the user agent switcher plugin for Firefox along with Firebug. The user agent plugin will let you spoof iPhone 3 user agent so you can see the mobile skin in the browser on your machine, then I would view the source of the page and maybe paste that into the wc3 validator to try and find out about any missing or extra tags, and I would also use Firebug to see whether any urls involved in building the page are failing to load, ie scripts or css etc., and also find out if any script errors are happening.
Not sure how long ago you implemented your custom module but I would also recommend updating it to use the newer container panels if you haven't already.
Hope that helps,
Joe