The time averaging of properties seems to be broken when performing replica exchange simulations. This is not a critical bug, as the affected properties (Cv and U) are typically calculated using the energy histograms for these simulations, and these work correctly. It is probably due to a miscounting of the time passed in each simulation after a swap.
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This appears to be due to DynamO forgetting to tell the output plugins about any accumulated free stream time from cell events. It looks like this needs to be removed from DynamO (it will simplify the code somewhat too).