The only reason it would do that from in the game is if it failed to make the download happen or found the directory to be unwritable. It could be that shadow directory stuff that Vista introduced. In that case, the thing to do is to make sure that your personal user account, as well as administrators in general, are granted full write permissions to the AI War game directory and all subdirectories.
But regardless, running it directly serves no function as all that tries to do is find updatelist.txt and then unzip whatever zip files are specified in that text file. The updater itself downloads nothing and has no more sophisticated logic than that.