I think I've narrowed down my problem re being unable to download windows updates autmatically to a javascript error in IE. I've located the most recently available javascript file for IE via the Microsoft Downloads site and its the same version as my apparent corrupted one, I found the old file in System32 there as jscriptdll.
So, I've downloaded the javascript file from the download site and can I now just install this new file? Its an .exe file and is self installing.
Thanks folk