The executable at this point has been created by InnoSetup, a widely spread setup engine, so this problem is somewhere part of InnoSetup, not yet of our own code.
I think there are two things to try out there:
the MSI installer, using Microsofts Installation engine to install Spybot-S&D. Since that's a completely different installation environment, the problem shouldn't appear there.
A second thing would be that InnoSetup 5.2 is out now (the Spybot installer was created with a 5.1 version). I can create a new Spybot installer using this new version of the installer engine, hoping that this problem no longer occurs with that version. Going to create a new installer over the weekend anyway for all the beta stuff
As far the error occuring when trying to update (to2012... even though you write about "exactly" the same problem there, it's a completely different executable affected!), that affects one of our own executables. If it runs from the start menu though, that lets me wonder whether you've got a 64 bit Windows version? Just because usually, the way it is started should be the same, but on 64 bit Windows, it's different whether started from the start menu (64 bit) or any 32 bit application. This shouldn't cause any problems, but if malware has infected one of these two ways...