Was it just a whiff of smoke or lots?
When you opened the cap on the downstairs fireplace it might have let the chimney start drafting on it's own but when it was closed it might have had a slight downdraft going because it was cool pulling some smoke down...?
Does it start smoking again when you close it again?
Is smoke only coming out the correct flue at the top or can you see smoke coming out of the one for basement fireplace too?
Are these chimneys on an exterior wall of the house?
Sorry for all the questions