Scaro,
You still haven't replied to a couple of the Questions:
1. What type of ac is it?
2. What are your actual differences in stall speed? (10% at around 30kts would seem virtually insignificant)
An observation:
1. A stall is never defined (to my knowledge) as being defined by the location of the elevator or stick. It is the point where significant boundary layer flow separates from the wing and does not reattach, hence causing a steep decline in the L/D relationship.
Some thoughts:
1. Aerofoil Section: As has been pointed out in several replies the aerofoil section is absolutely critical to stall characteristics. The LE being the most critical element. Any slight deformation causing a rapid loss in chordwise positive pressure gradient could trigger a separation and stall. The surface of your LE is also critical as any difference in smoothness will obviously alter the transition to turbulence and therefore the ability of the flow to remain attached. Is the surface absolutely identical? Are you working at low Reynolds Number where laminar flow is even more critical?
2. Engine Thrust: Can you be certain that the engines produce identical power? Are the props identical to transfer all the energy? A small difference in flow over the inboard wing at 30ins fuselage, where you suggest stall begins could have a huge effect on stall speed.
3. Test Aircraft Plastic Wing Deformation: A long shot but has the ac been subjected to loads that may have plastically deformed the wings during frequent high loading? (The thinner section you mention will effect the pressure profile certainly as well) can you be sure that the aerofoil section does not deform in flight different to the other ac? More info required on the ac structures and flight profiles I think!
4. CofG Vs Mass distribution: An equal CofG does not necessarily mean an equal mass distribution. It just means that the average of the masses is in the same location. You may need to investigate the mass distribution of your ac about the wings and the fuselage. Can you take the wings off to test? For example if the Mass is distributed more outboard on the wings on one ac then you can expect a different wing pressure planform and thus stalling characteristics.
5. Some possible tests and some slightly more crazy ones: I am not sure how much money/time you have or the legalities of these suggestions, but I am sure you can find out if you are that desperate! Take the wings off and find the CofG of the fuselage and Wings separately. Swop the wings over on the 2 ac!!?? Even just to reweigh! Can you swop the engines? Get an accurate readout of thrust at least for the 2 engines at idle.
Regards