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Using the IDFs on your E+ issue I tried changing the timestep from 6 to 60 and to 1 hour and got this results:

image description

As it an can be seen in the image, by changing the timestep to 1 per minute the air balance of the zones resembles that of the no-mixing scenario for zone 1, while zone 2 is brought up to zone 1 temperatures. This is the expected effect of mixing air between a zone significantly bigger than other with high air mixing values. I also simulated with a bigger timestep (1 per hour) and the result was even "worse" zone 1 and 2 temperatures, with less peaks than they should have.

I might be wrong, but my original idea is reflected there: With very high air mixing values, the small zone is transmitting more heat than what it has if the timestep is not small enough, as the air balance for the SOURCE zone is done in timestep t+1 while the receiving zone is done on timsetep t. Another way of understanding it is that if the timestep is too big, air at a certain temperature is being created on the small zones. This creates the "stabilizing" effect that is seen with big timesteps, as it is like giving it much higher thermal mass each timestep for GIVING heat, but not for receiving it.

Thus, it does not seem like a bug, rather an oversight that no part of the software checks if "more air is being mixed out of a zone than that of the zone itself in each timestep".