You can do some trouble-shooting of your own, relatively easily. But I agree, something is definitely up.
First, you can check for dragging brakes. Simply ride at 45 mph or better for a mile or so without applying the brakes. Then pull over in a safe place applying the brakes as little as possible. Use gears to slow down and only apply the brakes, if necessary, to come to a complete stop. Then use an infra-red temperature gun, if you have one. Or, I just use the back of my hand, holding it near, but not touching the rotor. The back of your hand is much more temperature sensitive than your palm or fingers. If the rotors are hot (they shouldn't be, but that's why we are checking) they can burn you.
If you do not feel any real heat at the back of your hand, quickly touch the rotor with a finger. If it is hot, you will be able to tell without doing any damage. The rotor should be cool to the touch. Repeat for each rotor. All should be cool. If one or more are too hot to touch, you have a dragging caliper and this can certainly create the issue you are having.
It would be good to know how long after the new rotors are mounted that you start having this issue. I find it unlikely that you have 2 bad hubs. So if both rotors are going bad, twice, it sounds more like a heat issue than a mechanical issue. I just don't think it likely you have 2 bad hubs. Or, are they just replacing both rotors as a matter of course? Only one being bad. That doesn't sound likely either. No reason to replace both if only 1 is bad.
Are they doing a dial indicator run out test to verify that the rotors are warped, as JayBros suggests? Is it both rotors? Or just 1? And do they take a similar reading after installing the new rotors? This might give indication of a bad hub as it should show up in some rotor deflection immediately.
Typically, if it is a bad hub, the problem will set in fairly quickly. Immediately, in many cases, depending on how bad the hub is. Not saying it isn't a hub issue. Just saying it may be a less likely possibility.
You don't say how you are riding your Spyder. Your surprise at this issue leads me to believe that you're riding style, loading, areas ridden, etc., have not changed enough to warrant this problem. But it is a different machine. And that may be a contributing factor if it is a heat related issue.
I will say that if your problem turns out to be heat, and not mechanical, EBC rotors may well be your salvation. I've had owners who have gone through as many as 3 sets of OEM rotors (heat caused warpage) that went to the EBC rotors and never had any more issues. The EBC rotors not only stop better, but are much more warp resistant than the OEM rotors. And, they are less expensive. Pretty much a no-brainer there.
It will be quite interesting to know what your solution is. I hope you will post it here.
