Are you sure Chassis1 is the other viper? Does chassis1 change at all, as its probably the water pump, if u pluged that into a normal header it will read the pumps speed, if you have a pwr_header, plug the pump into that, as the pwr one can't be controlled.
I have 3 case fans connected to my mobo 2 split and 1 not, then i have 2 vipers using the pwm cable, both are run by the cpu header, and only shows 1 rpm for both.
The vipers will only show as cpu in AI, if you pluged them in as i said earlier, that other reading is either another fan, or the h50 pump.
Set the vipers to run 100% by going into fanxpert, and go into profile and and choose disaple, this will ramp them up fully. Then check to see if both fans are spinning at the same speed, by looking at them, a hassle i know, but will put ur mind at ease.