It surely sounds like a frequency calibration problem, but it is also uncertain as to which piece of equipment contributes more to the error, i.e. the μBITX or your frequency counter,.
What I would do:
1) Use the calibration tool of WSJT-x to check my μBITX against a frequency/time standard station at the highest frequency I could get a clean signal from (14.996 MHz here from the Russian station). Note down the offset.
2) Do the same as in 1), but this time using my other rig in TX mode as a frequency generator and adjusting the dial frequency as to get the same offset as in 1).
3) The scope of step 2) is to establish a local frequency source of suitable power to be measured by the frequency counter, thing to be done here.
4) By now I would have 3 numbers:
a) The dial frequency of μBITX
b) The offset of WSJT-x calibration tool
c) The indication of the frequency counter
Enough information to allocate both (?) frequency offsets.
73 Nikos SV1IYF