Ever since upgrading to Windows Vista, I've had a probably with a program that I run infrequently where I'd get a message of "The Publisher Could Not Be Verified" and have to click on a box to verify I want to run the program. Since I don't use the application very frequently, the annoyance was minor.
Today I found myself needing to frequently re-load the application, so this message became really annoying. Windows Vista has an "Unblock" function in the file properties (right-click on the file from Windows Explorer and select "Properties"—it's on the general tab,) but this was not working for me.
I could click the "Unblock" button and apply the change, but the change wouldn't ever take. Since this program is my Program Files (x86) folder, I suspected this was the culprit. While I tried a few things to try to make the change as an admin (such as changing the file attributes—which forces you to grant admin privileges) the thing that end up working for me was to copy the files to another folder (like the desktop) go through the "Unblock" procedure again and then copy the files back to it's sub-folder in the Program Files (x86) folder. This seemed to do the trick.
So, while I'm sure there's a better way to get this to work, if you're getting the message "The Publisher Could Not Be Verified" every time you try to run a program and just using the "Unblock" function doesn't work, try moving the file to a folder that doesn't need administration privileges to modify the file.