A belated welcome aboard SCaro, and an interesting problem you have there. Sorry if I sounded a little patronising, but it's not always possible when somebody appears in the FT forum to gauge how much of a "grown up" they necessarily are.
A couple of thoughts...
- I used to own a little composite canard single seater, and have flown a couple of others of the same type. A common problem on that was differing washout between wings/aircraft which could alter both stall characteristics and trim. Any risk this might be a player?
- Presumably the CG values are similar? I've previously seen two otherwise identical aeroplanes (single engine, high wing) show quite different stalling speeds as a result of differing CG values. (Fwd CG leading to higher Vs).
I'll admit those are longshots. I shall go away and think....
G