There is most likely a slider in the wrong position for tray two. This makes the printer think you have a custom paper size loaded and will not match what your computer is sending to it. When no trays match then the printer will go off of the closest option or the last tray and prompt the user to confirm what they want the printer to do.
Heres what I suggest:
1. Check the paper guides/sliders on tray 2, make sure they are clicked into the correct position.
2. Still not working? Print off a configuration page and attach it to the forum so we can review your configuration.