I have been successful in getting CAT control of my radio via Ham Radio Deluxe. I am able to control the frequency via HRD, but when in the CAT mode, my VFO on the radio is inoperative. Therefore, I have to search for new frequencies using HRD instead of being able to tune the bands with the radio VFO. So, I have to disconnect HRD, tune the band for a new contact, then re-connect HRD to do the logging of the contact. Using my KX3 and HRD, I can tune the band with HRD or my radio's VFO. I wonder if anyone else has had this issue and if so how the solved it.
I’ve not used the CAT connectivity on a Yaesu in years and never controlled frequency with it, but it looks to me as though your program is sending a CAT ON command before sending the frequency but not sending a subsequent CAT OFF command.