Winstep applications store settings in the Windows Registry.
Settings are stored on the 'current user' registry hive, so each different user on the same computer can have his own individual settings and preferences:
HKEY_CURRENT_USER\Software\WinSTEP2000
Actual themes, bitmaps, icons, etc, are shared between all users.
C:\Users\Public\Documents\WinStep
So, this information should be enough for you to start digging for answers regarding what might be going on in your system.
When reporting an issue, especially one such as this that is obviously not a bug with the application itself but a system specific issue, and even more important when you consider that you are running your system in a non-standard way (running as admin the whole time), all details are important if you expect me to be able to help.
When trying to understand what is happening, I don't want to feel like I'm trying to extract a tooth from you.
...so please start volunteering information in a very detailed and prolific way from now on - and do your own testing too.It could be a registry access issue during boot (what happens if, after restoring the settings, you exit the application and run it again?), could be a problem with the user the application is running under (less likely, I think) or could be a problem with the data (or finding its location) itself.
A screenshot of what you are seeing right after boot is always a good idea too - a picture is worth a thousand words. You don't even make it clear if what appears is the default theme or no theme at all. And what about the actual dock contents, etc...? Do those change too?
Also, did you move the Public Documents folder to a different drive or location?