Down Draft from Second Chimney Flue

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Ok so after some changes, the downdrafting issue has improved a lot. I blocked off the attic fan using a thin piece of underlayment with strong magnets and some weather stripping so I can take it on and off easier. I also sealed around a lot of the holes on the 1st floor ceiling (not the basement) using spray foam, particularly around the chimney! I can't believe how much air was leaking into the attic from the basement two stories below by sneaking around the chimney. I suspect this will help keep my house warm in the winter as well.

The chimney still downdrafts but not as much, so thank you begreen for the suggestion - definitely would not have considered this otherwise. I also noticed that the downdrafting effect is greater when I have my central air running. When its off, I get much less smoke on the main floor.

I just bought a flue extender for the basement chimney to rise up above the other chimney cap as suggested by a few of you folks. I'll let everyone know if that fixes the problem once and for all. Thanks again for everyone's advice!
Why are you running your central air and your stove at the same time ??
Do you have a split personality ?? Lol
 
Why are you running your central air and your stove at the same time ??
Do you have a split personality ?? Lol
I was running them both to try to circulate the warm air throughout the house - the heat form the basement stove doesn't move well to the upper story of the house on its own so I was was hoping the central blower would circulate it better (this is just the blower fan running, not the furnace heat). Unfortunately, this did not see to be very effective and just caused the upstairs chimney to draft.

With that said, i installed the flue extender and leave the central blower fan off, and have not had any down drafting issues since, so thank you everyone for the advice!