Hey Durango Joe,
I own a chocolate/pastry company in Telluride - right up the road from Durango and also at 10,000 feet and have baked up here for 14 years so these are my suggestions.
All kinds of cakes I've had plenty of trouble with up here until I adjusted the recipee. However, I've never had trouble with flourless cakes at altitude except when I did them in a convection oven. Are you baking the cake in a convection oven?
Also, check the temp on your oven - is it accurate? Temperature is critical with flourless. My flourless chocolate cake does rise very high and then fall to a lower level after it cools. I'm not sure, but I think this is the way flourless cakes work - can't remember doing them at a lower altitude - I've lived up here for 14 years.
Additionally, at this altitude I find that other factors in weather affect cakes - especially barometric pressure. Other bakers up here have noticed this also. I have one genoise that won't work at all if it's raining. Have you only made this once? What was the weather?
On another note - I may be needing a pastry chef in a few months. Do you know anyone interested?