It sounds like you might have boot sector virus protection enabled in the BIOS. This is something that should always be disabled as it will interfere with Windows. It will probably not be named exactly as above but almost certainly will be in your setup options and will include the word "virus".
Depending on your machine, getting into BIOS setup may or may not be simple. With an AMI, Award, or Phoenix, press Delete as soon as the RAM test finishes. With others, you might have to search for the key or key combination. This site has some others listed: http://www.mustek.com/Support/techdocs/bios.html
My brother gave me his old computer running Win98se. I was going to network it to my system running XP Pro with sp2 installed. The trouble is that the hard drive in his old computer won't boot into windows. After it starts to boot a window pops up stating that there was a boot virus detected and then it refuse to go any further. An ideas on how to get rid of the boot virus without losing all the data on the hard drive? Can I some how create a bootable floppy that will get rid of the virus and save me the trouble of having to reformat the hard drive?