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