Reactive mobile design works in emulation, but not devices

I am making a website for my Boy Scout Troop, and it is employing a responsive design to make navigation simpler on small screens. It works perfectly when resizing a desktop browser, as well as on device emulators (I have tried it on several, and for a variety of devices), but it is not reactive on actual devices, including IPhones, IPods, and Androids, using either default, or 3rd party browsers. I can not figure out any reasons why this would happen. The only differences I know of between a device and an emulator is the User Agent string, which I use to handle IE separately (I am still debugging the reactive design for IE, and am having issues, but that is a seperate topic), but should not effect anything else excpet possibly on a Windows phone.



The URL for the website is: http://bsatroop159.org

Note: You may notice several small errors such as a page being pushed toward one side, or an image leaving it's bounds, but I have actually fixed those, I just need to send in the patch still.

The opening line of the CSS for my media queries looks like:

@media handheld, only screen and (max-width: 725px)

A possibly relevant segment of my JavaScript:

function isIE(){
                var ua = window.navigator.userAgent;
                var older_ie_ua = ua.indexOf('MSIE ');
                var newer_ie_ua = ua.indexOf('Trident/');

                if ((older_ie_ua > -1) || (newer_ie_ua > -1)) {
                    return true;
                }
                return false;


            }
            function setViewingMode()
            {               
                    //Screen Sizes
                    var width = document.documentElement.clientWidth;
                    var WinHeight = document.documentElement.clientHeight;
                    //Make sure this matches the media queries in the CSS files CSS_Reactive_Designing and CSS_SimpleGrid
                    var minWidth = 725;
                    //&&  navigator.appName != 'Microsoft Internet Explorer' needed while mobile mode not working in IE
                    if(width <= minWidth &&  isIE() != true) {//This Qualifies for special mobile site mode
                        DesktopNavigator = document.getElementById('non_mobile_only_element');
                        DesktopNavigator.style.display="none";

                        MobileNavigator = document.getElementById('mobile_only_element');
                        MobileNavigator.style.visibility="visible"; 
                        MobileNavigator.style.display = "block"; 

                        var dsoctop=document.all? iebody.scrollTop : pageYOffset;
                        makeTall = document.getElementById('mp-menu');
                        makeTall.style.height= (WinHeight)+"px";
                        makeTall.style.top= (dsoctop)+"px";
                        pusher = document.getElementById('mp-pusher');
                        pusher.style.paddingLeft="0px";                                             
                    } 
                    else{//This uses the standard website mode

                        DesktopNavigator = document.getElementById('non_mobile_only_element');
                        DesktopNavigator.style.display="block";

                        MobileNavigator = document.getElementById('mobile_only_element');
                        MobileNavigator.style.visibility = "hidden"; 
                        MobileNavigator.style.display="none";   

                        pusher = document.getElementById('mp-pusher');
                        pusher.style.paddingLeft="0px";                     
                    }
                }
            setViewingMode();
        </script>

I can add more code to the question if someone hints at anything else that may be relevant, or I can remove some if what I have is just cluttering the page. I would really appreciate any help with this, as this is a pretty major issue, and I spent a long time making it reactive. I tried everything I could think of to fix it, but honestly, I could not think of much (not sure what could be the culprit). Thanks ahead of time for any help.