You mention two points from the text that I have revolved around in my head before.

First, we know Elinor is supposed to have good judgement, but how, exactly, could she tell the difference between an oppression of spirits, and a natural gloominess? Especially since the Colonel's darkness never seems to break a little light onto his thoughts.

Second, if Sir John drops hints, and Mrs. Jennings does not immediately start in on him to tell the whole, then that could only mean that Mrs. Jennings was not in the room! I think this has to mean that Sir John brings it up when she is not around, a sign of great friendship for Col. Brandon, since normally he seems to air everyone's laundry whenever he can.