Another thing I've noticed that you could possibly ask your tech about.
There is a stacker NVM procedure that calibrates the stacker, try seeing if they can show you how to run it.
Also, if you have multiple stacker carts, they may vary minutely and can cause stacking issues. Sounds dumb, but I have solved stacking problems before just by changing my cart out (since the stacker was calibrated with one cart in and not the other.)
If you have more problems next best bet is to send to the top tray. I have been able to run 20x14 18pt C2S through my stacker and it was fine, however.