"For QAVION our selected margin on the FMSCDU PERF page is 1.3g."
Hmmm.... In which case, this sounds unlikely to be your problem. From memory, the FMC defaults to 1.2, which would mean the yellow band would go down, not up.
Unfortunately, this is a very complex system... too many variables/components to consider: AOA (vanes and associated heaters), airspeed(CADC's), flap position(FCU inputs), gear position(PSEU input) and speedbrake handle position (APFD?) are all inputs to the (two) MAWEA stall warning cards (SWMC's). Boeing have said in the past that AOA will tend to give the largest error. +1 degree can give a 5 to 10 kt error, but if only one vane is u/s, then the red brick values would be different on the Capt's and F/O's displays. Note however, that the manoeuvre margins would be the same... as the FMC's use the greater of the computed stall speeds (from the two SWMC's) to calculate manoeuvre margin.....at least this is the way it works with the flaps out of up.
I'm just wondering what effect the Fifth Pod and Gear Down dispatch switches in the MEC have on manoeuvre margins.... Would this also raise the flap markers as well as the stall speeds and manoeuvre margins?
The puzzling thing is the fact that you have this problem throughout the fleet. Sounds like a software thing... or someone's been fitting wrong dash number computers to your aircraft.
Methinks you need Boeing's expert help here.... ;-)
Good luck!
Rgds.
Q.