Are IE 11 users not able to download PDFs and does the following error occur if they wait long enough?
Adobe Reader: A network error occurred while accessing this document on the internet
In 9.1SP3 CU5, Ektron handlers were modified to allow HTTP range requests. While this is a nice feature for downloading large files it opened up the possibility for new issues like the above one with Adobe Reader. The issue is more common with sites on Server 2008R2 than sites on Server 2012.
To resolve this update Ektron to 9.2SP2 CU15.