1997 Honda Odyssey brake question

1997 Honda Odyssey mileage: 81,340. I had installed Honda brake pads replaced in October, 1999. Ever since then, my brakes have not felt right. I installed honda brake rotors and they kind of feel warped? I took it back to have them look at it again and they said it sounds like a brake problem and when I told them that they just replaced my brakes a few months ago, after looking at it, they decided that my problem was not a brake problem and that they didn't know what was causing the problem but that it was not a brake problem. Today, I took my car to another repair place and they told me that whomever did my original brake job cut my new honda brake rotors too thin. He said 2500's to 3000's under the legal spec. And that my rotors are bad and need to be replaced. Is it possible to cut them too thin, and if so, what problems could that cause. And is there a way to know and/or prove that they were cut too thin?