+ AA6YQ comments below
Similar issue here, all was working perfectly with previous version, WSJT, FLDigi and MRP40 all playing nicely with Commander. After updating SmartSDR anything triggering the PTT via Commander made it stay on until MOX was pressed. Even using Commander itself had the same effect. Only workaround I have found is to set the radio in Commander to Kenwood, only issue is mode switching doesn’t work as Kenwood don’t have a DIGI-U mode.
Hope this helps till a new version of Commander comes out.
+ Yesterday, I "upgraded" my 6500 to SmartSDR v3, did some testing, and sent my observations to the Flex engineers with whom I am working.