Are you sure that in not the crystal for the CH340 USB to serial?
All the Nanos I have the MPU crystal is on the front (side where the atmel MEGA328P many legged chip is).
The likely cause of the 1khz offset is likely either BFO incorrectly set, or cumulative error in the math.
From memory the frequencies calculated and displayed are based on 5351 output frequencies and
would match the Zero beat frequency (if cal in correct) and do mot match the filter center channel