I have the exact same problem with my front rotors as you do. Did you buy them off ebay from this guy [tmax500hk] I do know I should have replaced the pads, but didnt this time. The vibration was real bad when I first put them on, so I rotated them a 1/4 turn on the hub and it got a lot better. I still need to pull the wheel and throw the stock rotors on to verify that they are warped, cause I still think they are.
Anyway, I contacted the seller and he said he couldnt give me a refund on the rotors, but said the best he could do was sell me another set for $70 off. Reason being is that they were probably dropped in shipping, cause the package they came in looked like **** and was not boxed properly when I received them. I paid "him" $50 to ship them and he didnt take the time to package the rotors right and says its my problem to contact the post office to make a claim. And to do so I had to have the package that it came in. WTF, I threw the flimsy ass scuffed up cardboard in the trash as soon as I opened it. Regardless, I'm not happy with this rotor seller on ebay and won't buy another set from him, even if he does give me a discount. Good luck with your similar issue!