Prototype.js issues with Select elements

I ran into a strange bug at work today - on a form with a couple of select boxes with some buttons which swap elements between them a tester reported that some of the boxes were simply disappearing when he clicked on the buttons (though strangely, only in IE). After some digging around I discovered it was related to the Element.remove() method in the prototype javascript library - it was replacing the native remove method on the select element and removing the whole thing. Eventually I discovered this bug report which explained the issue, after that it was simply a case of trawling through all the code and finding all the places where I referenced the select elements using the $() function.