I had the same problem (Thermostat = 69, ISY=65, recently replaced PLM, motion control sensors to change thermostat temps based on room occupancy)... For the last several days, my ISY was showing 0 degrees but programs appeared to all work properly....
SOLUTION . . . I “restored” the Thermostat (right mouse click in ISY) and then sent updates to the device... it has been 12 hours and they remain sychronized...