This is a minor, esoteric problem and not a showstopper, but I'm wondering what other VS2008 idiosyncrasies are out there.
If you make a web app, add a textbox and run a focus function for the textbox on page load, it works when you run VS not as administrator from a Vista non-administrator account or if you run the page from a browser instance run on its own, not from VS.
If you browse the page from VS as Admin, the focus doesn't work. This for Cassini and from the local IIS.
Stuff like this just makes me trust VS a tad less.
As in the comments, this was my own bloody fault. I found the problem, as my ie security was set differently for the admin account which had Javascript disabled.