So I took a different approach and decided to change uploadify to use HTML5 upload instead. It appears to be working, though is lacking a few things:
1) No error reporting
2) No upload cancel
3) I've only tested it in Google Chrome
4) Progress meter is text (e.g. 30%) instead of a progress bar
5) Some of the events still rely on the existence in the DOM of the flash uploadify elements, which I've hidden visually
@VRoxane I still get the same HTTP Error on only one server now. Download the latest code and see if that will help some of your issues. After I upgraded, used the UploadifyField::disable_authentication() in the config file...all my sites (except one) were fixed.
Another thing to think about...is this will most likely be no issue once 3.0 comes out. Keep that in mind as well.
Let me know if upgrading helped you...and if not then I will try to help as much as I can.