My Altered did the same thing. I run a Enderle methanol injected 434sbc but with no supercharger,just a tunnel ram. It always runs great but when I added nitrous it started popping on the top end. I never added any extra fuel when I installed the nitrous,I just added a single spray bar in the tunnel ram with a 100hp jet and about the 1100ft mark she started popping. To me it was running lean. So maybe your engine is running lean also.
Just a thought.