That honestly has crossed my mind. I took off the springs I had because they had a ton of passes on them. Pressure wise they were in great shape but they were PSI and I have heard they hold their pressure right up till they break. Anyway, The old springs were set up about .065 from coil bind. These new ones are about .125 if I remember right and have about 25 pounds more pressure on the seat.
As you know, when the brake loads the engine on the dyno, things can get interesting in a hurry. One other thing is to check with the dyno shop and see where the water brake servo was at for percentage of load. Ideally, you want it to be at 90%. If it's not, harmonics can be induced because of the lost 'dampening effect'. The fact that it's happening at random RPM ranges makes me wonder.....
Can you post a pic of the BSFC numbers and lbs of fuel/hr. numbers on the different pulls?
Honestly, if nothing else comes to light as a cause, I'd put the old springs back on and take it back to the dyno. Too bad you weren't closer.
On the dyno last week with this 283 NHRA Stock Eliminator engine. Big power, big problems.