I have just received a response from Winstep Support. I had already ensured the compatability and Nexus preferences startup settings were unticked but the problem still exists. Here is the response:
The reason none of the other users replied is because this is not a problem with the application per se (i.e,; none of them have seen it before), but something to do with HOW the application is being launched at start up. Probably something you did by accident or something else interacting with Nexus Ultimate.
For instance, reading back on your emails, you ended up figuring out that the Access Violation error you were getting was caused by buggy context menu handlers. These context menu handlers are provided by 3rd party applications but run within the process of the application that invokes them - if they are buggy and crash, they take down the host application with it as well (in this case, Nexus Ultimate). So, even though the error seems to be a bug in Nexus Ultimate, it really is a bug in a 3rd party application.
Worse, since it is something specific to your system and the software installed in it, figuring out exactly what is causing a crash like this can sometimes be a trial-and-error nightmare - and normally only the user himself can figure it out.
Regarding this particular UAC problem, at some point, somewhere, you must have specified that the Nexus Ultimate executable needs high privileges to run (e.g.; run this program as an administrator).
The first thing you should do to figure this out is to go to the Winstep folder in C:\Program Files (x86)\Winstep\ and right click the nexus-ultimate.exe executable. In the context menu that pops up, select Properties. In the Properties dialog go the Compatibility tab. At the bottom (well, at least under Windows 7 you have this option, don't have Vista here anymore to try this out) there should be a 'Run this program as an administrator' option. Is it checked? If so, there's your culprit, please uncheck it.
If that doesn't work, instead of running Nexus Ultimate via the built-in 'Run at startup' setting, try disabling that setting in Nexus Preferences, and adding a shortcut to Nexus Ultimate in the Startup group of the Start Menu.