I wonder if there is some low level audio-frequency warble/buzz/hum/tone in LSB transmit only that is affecting the frequency counter throwing the reading off.
Try listening to the transmit of both the LSB and USB on a good receiver, preferably with headphones and see if you can hear artifacts on LSB that aren't present in USB.
Try listening to the transmit of both the LSB and USB on a good receiver, preferably with headphones and see if you can hear artifacts on LSB that aren't present in USB.