Hi,
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.

In compatibility mode, IE gave below description;

System.InvalidCastException: Error 0x17E0. Hata ayıklama kaynak dizeleri kullanılamıyor. Bkz. http://go.microsoft.com/fwlink/?linkid=106663&Version=5.1.20513.0&File=mscorrc.dll&Key=0x17E0
konum System.Windows.Browser.ManagedObjectInfo.Invoke(ManagedObject obj, InvokeType invokeType, String memberName, ScriptParam[] args)
konum System.Windows.Hosting.ManagedHost.InvokeScriptableMember(IntPtr pHandle, Int32 nMemberID, Int32 nInvokeType, Int32 nArgCount, ScriptParam[] pArgs, ScriptParam& pResult, ExceptionInfo& pExcepInfo)
Satır: 1
char: 4182
Kod: 0
URI: http://…….com/wp-includes/js/plupload/plupload.silverlight.js?ver=1.5.5

I hope, this info assists you to find a solution.
Regards

Open WP Project Manager plugins /js/upload.js and remove silverlight from line 20. It should now read this: runtimes: 'html5,flash,html4',. Now Check if the problem is still occuring.

Hi Tareq,
I did what you wrote.
It worked at IE8 , only.
Unfortunately, at IE9/10, issue is going on.
Thanks fro your cooperation.
Regards

Correction:
sorry. It works at IE8/9 properly.
It doesn’t work at IE10.

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.
Regards

I couldn’t also find the reason why it’s not working at IE10. May be you can also remove the flash parameter. If by any chance you find a solution, let me know.

When I removed the flash from upload.js, unfortunately It doesn’t work both IE9 and IE10.