I'm unable to reproduce any problem here. Add this line and tell me what you see in the Event Log:
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log "mode is " & hvac mode of device "YourThermoName"
Are you changing the mode using Indigo or at the thermostat itself? It can take up to a minute or so before the thermostat adapter will report any mode changes at the thermostat itself (even though you are polling it). There is a lag between when the Venstar thermostat changes modes (or setpoints) and when the adapter knows about that change.
But if the Event Log is showing it is heatOn and so is the Event Log, then I'm not sure what is wrong. You should get the same value via AppleScript as shown in Indigo's UI.
Matt