Hello Phil
I too have a Flex-1500 but config WSJT-X direct as I do with many other radios, I don't use FLRig as part of the setup, as I'm not doing remote control, and it works without issue.
I was curious, so downloaded FLRig and using the TS-2000 setting in FLRig, and FLRig FLRig in WSJT-X I too see WSJT-X changing sideband. However I notice when selecting the TS-2000 rig the only option for data out is FSK and FSK-R, if I select USB no audio goes to WSJT-X.
Are you using specific rig definition file Phil?
Regards
Glen