IE9 seems to have a bug with SWFUpload embeds, whereby if you try to call "getAttribute / removeAttribute / setAttribute" on the element, an "object expected" error is raised. And I found that the cleanUp() function in the swfupload.js remove all the js functions including "getAttribute / removeAttribute / setAttribute" from the object DOM in IE9.
To fix this issue
In SWFUpload.prototype.cleanUp
Change:
if (typeof (movieElement[key]) === "function")
To:
if (typeof (movieElement[key]) === "function" && key[0] <= 'Z') // Remove only Flash functions (starts with capital letters).
Patched version of uploadify is kept at this location
http://www.dariowiz.com/scripts/jquery.uploadify3.1Fixed.js
Regards.