I have $('#just').hide()
SWFUpload's button's containing div, and the actual upload immediately stopped.
What is the reason for it? The debug said nothing.
Update: interestingly in IE7 it does not stop.
I had the exact same problem. I needed to hide the button. I tried this (when the upload starts, i.e. bind this to uploadStart event:
$(".swfupload").css("visibility", "hidden");
That worked!