Probably a harmonic issue. Something about the combination of springs, pushrod, rocker arms and lobe and the RPM. Something as simple as changing to a stiffer pushrod might solve it but without spintron time you won't know for sure. More likely you can solve it by going with a less aggressive cam lobe and taking some spring pressure out of it.

I think the Indy R1 is a Comp grind but it has been a few years since I looked at one. If it uses Comp lobes then you could talk to Comp tech line and ask about spring pressures. The guys at T&D also might have some ideas. What pushrods are you running? If they aren't 7/16 or 1/2 inch then you might want to try that first.