The QSO data coming from JTAlertX contains the Freq value in MHZ as per the ADIF standard. It is stored in the QSO Relay SQLite file as KHz which is how Log4OM stores it, and it is relayed to HRD as Hz which is how is it stored there.
We cannot reproduce the problem you report, and no other users have reported anything similar as well. So all I can suggest at the moment is that the frequency was not obtained correctly from your transceiver via CAT control by WSJT-X.
You could open the WSJT-X log directory by selecting 'Open log directory' from the 'File' menu, and open the 'wsjtx.log' file and see what frequency was logged there for that QSO. Here is a sample from my 'wsjtx.log' file:
2017-Apr-03,05:09,4W/YB3LZ,PI21,14.078307,JT65,-17,-17,,JT65 Sent: -17 Rcvd: -17,
And here is the same contact from my 'wsjtx_log.adi' file:
<call:8>4W/YB3LZ <gridsquare:4>PI21 <mode:4>JT65 <rst_sent:3>-17 <rst_rcvd:3>-17 <qso_date:8>20170403 <time_on:4>0509 <band:3>20m <freq:9>14.078307 <station_callsign:6>VK2BYI <my_gridsquare:6>QF55mx <comment:26>JT65 Sent: -17 Rcvd: -17 <eor>
As you can see the frequency is in MHz, and it was for a 20m contact on a calcuated RF frequency of 14.078307 MHz (my rig was tuned to 14.077). This has been converted to 14077 KHz and stored in the QSO Relay SQLite file, and was then converted to 14077000 HZ and stored in HRD Logbook which is displayed as 14.077.000.
If you wish, you can send my your 'wsjtx.log' or 'wsjtx_log.adi' files, along with the QSO Relay SQLite file and I will take a look for you.