I have IE 11 working to MCD6UR3 with the following settings tweaks:
Java 1.6_25 loaded, updates are disabled
IP address of MCD is added to Local Intranet site list in IE, "require HTTPS" is disabled
Security level for Intranet zone is set to "Low"
Pop-up blocker is off
Windows Firewall is off (if you can't turn it off, add exceptions for FTP on ports 20-21)
I don't know if all of these steps are required, but it's what works for me.