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That's what's causing the problem (overwriting program files folder). Those tools are installing specific info for whatever OS it's installing on. I don't have a 3dfx card (so I'm not sure if you can or not), but could you get away with not installing the tools? Maybe you can just install the driver and not run through the whole setup routine.
Also, you may want to look at a product like System Commander or Partition Magic. Both create/resize/move partitions and have a boot menu for OS choices at startup. Would definitely fix your problem unless hard drive space is an absolute premium and you can't afford the extra space.
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