Ok. So here is the hackity-hack solution I came up with (if you cant beat em -- and by em, I mean javascript, join em):
parent.document.getElementsByClassName("iframe_input")[0].click();
I just force a click on the first input element when the modal hides and this seems to resolve the behavior. That being said, this seems really hacky and Im all ears as to why this is wrong but it does work like a charm....