I would like to give more info about issue.
I use child theme of twenty twelve theme, and wp 3.5.1 ( also tried 3.6)
I try to upload files at IE8/9/10 at both compatibility mode and non-compatibility mode, but it doesn't upload file.
Media upload works properly, but file upload at your plugin doesn't work.
Some more info;
uplading is possible at compatibility mode of IE10, but it is not at non-compatibility mode.
I don't know why it is ok at IE9, nevertheless it is not ok at IE10.
I don't know how I can debug it to find the reason.
Thanks at advance your suport.