Did you try UFT before you put the patches on? I had no problem at all moving from 98 to XP and didn't even have to put patches on. As long as a person has 3.1, there shouldn't be a problem. HOWEVER ... there are those occasions when we see people have them.
Are you an international user? There is a different patch for that.
It may be that you have to just click ignore each time and live with it.