The many hours of investigation have finally rendered some results. Awkward results, but some results in any case.
I was able to reproduce the problem in a fresh Vista x86 VM, with VS2005, the latest ViEmu (2.2.6) and the latest Visual Assist (1647). After reproducing the problem, I tried setting up a full ViEmu dev environment, which involves installing VS.NET 2003 and a few additional tools, and the problem went away!
I did this again, and found that, indeed, installing VS.NET 2003 on the same machine seems to fix the issue. It makes it impossible for me to debug the issue, which would be a hard task in any case, but at least it solves it.
So I suggest that you install VS.NET 2003 on the same machine (I only installed Visual C++ support, not any of the other languages), and see whether that fixes the problem. Please let me know whether that works.
This is a tough issue. Event notification seems to work differently sometimes for no good reason, there is no documented dependency that would cause this. And the cause seems to be somewhere deepn in the bowels of Visual Studio, .NET or Windows itself. The fact that installing VS.NET 2003 fixes it leads me to believe there is some kind of dependency on system DLLs or .NET assemblies -- given Windows' fragile design, something in the VS.NET 2003 installation makes VS2005 behave differently, maybe loading another version of some DLL or .NET assembly. You can guess that trying to track the issue with such a subtle dependency is all but impossible. Hopefully the VS.NET 2003 is a viable solution to have it quickly corrected.
By the way, I also tested whether only installing VS.NET 2003's "prerequisites" fixes it, and it turns out it doesn't. You need to actually install VS.NET to fix it (and it's not necessary to even run it once for the magical effect to happen).