In my experience working with dom elements, if I'm having trouble getting an element, I typically try moving up in the hierarchy and seeing if I can get a parent (or a parent's parent).
What does this give you?
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myFrame := document.parentWindow.frames[1].document.body.innerHTML
msgbox % myFrame
Based on testing that I've done, this may/may not include the element you're looking for, but it will tell you if you're targeting the frame properly (by producing something), and, if you are, that will tell you that you that it may not be a frame issue, but, rather, it may relate to the input component of your javascript.
This targets the entire frame. If you can find something in the hierarchy between the whole frame and your target element, try getting that also.