I was able to find a solution for this one. Utilizing a code library to determine when I was on the iPad, I loaded a function that added an event that used Dojo to attach an onscroll event bound to the exterior form rather than the window itself. I had to embed this in a script block in my navigation custom control for some reason, it wouldn't attach if I put it elsewhere. Here's the code if anyone else needs it in the future.
dojo.ready( function() {
var object = dojo.byId('view:_id1')
//console.log(object);
dojo.connect(object, 'onscroll', this, function(event) {
// console.log('scroll');
var object1 = dojo.byId('#{id:adminDropDown}_ab_0_dropdown')
if (object1 != null) {
dojo.style(object1, "display", "none")
}
var object1 = dojo.byId('#{id:insDropDown}_ab_0_dropdown')
if (object1 != null) {
dojo.style(object1, "display", "none")
}
var object1 = dojo.byId('#{id:emDropDown}_ab_0_dropdown')
if (object1 != null) {
dojo.style(object1, "display", "none")
}
var object1 = dojo.byId('widget_view:_id1:DateEntry_dropdown')
if (object1 != null) {
dojo.style(object1, "display", "none")
}
});