The manufacturer will simply bundle the latest driver from nVidia, at the time of packaging, with your card. They could also include additional software with the driver. It is, however, better to use the latest drivers from nVidia themselves.
MSI drivers are Nvidias drivers, but generally with a little extra software added to the bundle as AKJ said. They are rarely up to date even on their website, so it is much better to get them directly from the nvidia website.
nividia's drivers always man and nothing else! I can tell you that my uncle recently bought a 7600gt and was using the supplied manufacturers drivers and had all kinds of problems until I told him to go to Nvidia's website and download the drivers from there. For whatever reason that did it and he has not had any problems since; that was 2 months ago.
The particular revision number of a set of drivers are all same, makes no difference where you get them, as Prozac stated.
By going directly to Nvidia's web site, you can be sure of getting the latest revison which probably included fixes that solved your uncles problem. The first couple of driver sets written for any new hardware are almost always certainly going to buggy until enough people run the hardware, complain about the problem, and the manufacturer releases new drivers to fix it. It also could be that the original install of the drivers may not have been done correctly. Usually what happens is people fail to completely uninstall all the old drivers and software from the previous card, and when he installed the second time, for whatever reason and circumstance, he got it right.