I've been noodling on where the CO could have come from too. The flight deck has its own dedicated plumbing and everything gets vented out through the cargo compartment, so it is unlikely anything from the passenger compartment or cargo area would flow up front.
If something were burning and producing enough CO to affect the pilots, I would have expected accompanying smoke or odor (which may not have been reported).
The best guess I can think of now is that a significant amount of engine or APU exhaust was being ingested by a compressor section while the aircraft was on the ground (or the ground air supply gassed them) ...
or they flew through a really big, rogue cloud of carbon monoxide during departure.
Or, the trace amount of CO detected after landing is a red herring.