Did you guys ever resolve the issue? I seem to be having the same problem, though I don't know if it's MSI Afterburner's fault. Anyway, my RPM's drop under use as well, only not by as much as yours. My fans are at 20% and usually idle at around the mid 990's, sometimes ramps up to the low 1000's but then drops back down to the 990's again. But once I load up a game, it drops to the 960's-970's, will sometimes ramp up to the 980's but then drop back down to the 970's. WHY?!?!
However, the temperatures seem okay. I ran Heaven Benchmark for about 45 minutes and it never went over 66C. I just don't understand why the fans are acting so screwy.
Btw I own an ASUS R9 280x (Radeon HD7970)