Using my calibrated Agilent 8924C analyzer I see OTH #51 vary by 1330 Hz from 0-100% when measuring the 124.032 MHz 2LO signal at P4. When transmitting on CW or AM at 20 MHz it varies 215 HZ from 0-100%.
In Maintenance mode, adjusting the REF setting from 0-FF changes the 124.032 MHz 2LO by 1300 Hz, but does not affect the TX frequency when returned to normal mode -- just as you saw.
I don't have an explanation for why it behaves that way. But if you have accurate frequency measurement equipment and follow the adjustment procedures, you should have adequate adjustment range in menu #51 to calibrate your TX/RX signal at UHF and below. You should verify that your DDS REF 2LO is at exactly 124.032 MHz. Then perhaps verify your RX frequency in normal mode by zero beating to a commercial transmitter at the highest frequency possible.
It is possible for the X1 VCTCXO reference oscillator to drift with age, but that would only be suspect if can't adjust the 2LO REF signal to 124.032 MHz in Maintenance mode.