The rx-v 3900 yamaha receiver should have no issues driving that system. It is perfectly compatible. You are also doing the correct thing in setting the yamaha to 8 ohms instead of the 4 ohm option.
The possible causes I can think of are a defective receiver, powering the receiver beyond its capabilities which is inducing clipping and damaging the speakers or maybe a underlying problem with electrical storms which damaged your receiver and or speakers (do you get these in India and if so have you had them lately?). Do you also like to listen to movies/music at what you consider very loud playback levels?
Very strange problem indeed. You might see 1 blown driver but you are blowing multiple drivers in multiple speakers. Are the tweeters functional? This is a rare case.
