I was baffled by this too. All a bit strange.
For uBitx V 4.3 calibration Here's what i did:
Change band to 20m, attach a dummyload, or a decent antenna for 20m, with a low SWR. Use Your frequency counter, then start the calibration routine - the radio will key up , then adjust so Your frequency counter reads bang on 20mhz.
After You do this, Things will be fall into place i suspect, including the BFO problems i bet You are having.
Yes, i know. This sounds wrong, but i could NOT get my uBitx to behave predictably until i did this. I actually thought i had fried it it was so unstable and off-frequency, then i did the calibration thing, but with the radio on 20m, and it all fell into place.
