interesting thread but my take on it is that its probably not the wood, but either the insert has problems or your flu has problems, I think you had it right in your first post if the longer flue did have a stronger draw the fire should be hotter wich would make your downstairs insert work a little better than your upstairs insert, ive read about stoves actually being more likely to overfire when the draw was excessive and its usually worse on epa stoves with some form of secondary burn because you cant close off the air to them as good.
assuming the insert is ok, I think that for some reason your upstairs flu is actually drawing better than your downstairs.
assuming the insert is ok, I think that for some reason your upstairs flu is actually drawing better than your downstairs.