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Since this is a new furnace the culprit is likely a loose connection. Check the electrical connections at the pressure switches all the way back to the board. Also check to be sure the vac tubing connected to the switches isn't kinked or disconnected
Possibly could affect draft pressure. Filling the traps is done to prevent any exhaust gases from escaping out the condensate drain.
I don't have my hands on the manual. This is not related to the question you posted.