I am experiencing similar problems with IE 11 users.

I have a multiple upload page. Today the user was uploading 3 files.

The upload failed on the first upload. The UploadCompleted was triggered in the code behind - but I see no evidence of the file arriving.

The first time the user got this error

SERVER SIDE EXCEPTION: failed to download 1094252-v1.wmv

System Exception: Invalid form data,last bounday not found:\xOD\xOA

at CuteWebUI.a.a(Http_Context A_0, HttpWorkerRequest A_1, etc etc

(I can email you the jpg screen capture if needed) 

It has been working flawlessly for months for Chrome users 

Gerald