Been playing around with this a bit more today after seeing error logs for PapyrusAssembler.exe in the event viewer. In the end I fixed the errors when compiling scripts within the ck by setting both papyrusassembler.exe and papyruscompiler.exe to "windows 7" option under compatibility mode. Just to note I am running windows 7, so if someone could explain the difference to me there I would appreciate it. I only use Windows for Skyrim and the CK so I'm not well versed in what the compatibility options actually change.