It sounds like you have indeed eliminated the full mark as being the trouble by charging on another charger and getting a low reading on the very first discharge cycle with the quattro. There are really only a couple of possibilities that I can come up with since the battery isn't any different and has whatever capacity it has. The trouble that your having seems to be akin to "what to label the pack" and I would guess that you are one of the very few who would see it as a problem. I suppose I am content with labeling the pack with whatever the equipment tells me at the time.
When I have two charger that do not agree I just make a note or take that info with a grain of salt when naming my pack.
Anyways back to the possibilities:
The current over time equals the capacity down to a given voltage. If the timer is right on the money and the current is exact then we only have the ending voltage to play with and it can very well be different pack voltages measured by 3 different chargers that are set the exact same way.
The timer should be very easy to check with a stop watch and the current should be easy if you have a way to measure it and it doesn't fluctuate a lot. If so then let's play with the bottom figure. What is the current and the ending volt cut-off of the 5 cell packs that you are using for discharge?