We have had the same problem. Installed the airfoil chaffer and saw a huge improvement in wheat. We still get chaff sometimes but very little grain loss. I think the chaff problem now is mostly on very windy days and the chaff is carried up the side of the machine and sucked into the fan then carried by clean grain dropping through the seive into the tank. We are going to try screen over the fan intake to see if this helps.
You might be right about the chaff through the fan. We always get some in the tank also when it is really windy. I used to think it blew in the grain bin directly, but through the fan makes some sense.