Keep at it, some of the patches are going to be going back to previous files and updating them as you progress, also what you may thing are the same files my just have the same starting information with different info being shown thats to long to be seen in the area that it displays in.
Even if your installing from the newests box set you are still going to have a lot of patche data and update data to install.
A suggestion, make sure to run a full file scan after you finish installing just to make sure that everyting is set up right. It will take a little more time but may just catch any problems in your install.
And please, reboot when all is said and done.
Its just good policy to do so after a massive install, cleans out the no longer needed temp information in your ram and will make it play a little smother on that system hog vista
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Given how little time we have, given all the things we have to do, can you really afford to play a game you don't enjoy?