The app doesn’t actually turn on the fan or the heat/cool - it merely sets parameters in the thermostat to define when the HVAC equipment runs.
It is more likely that you have more than 1 SmartApp setting parameters, or that you perhaps set the change frequency in the Smart Circulation Helper SmartApp to low - the default is 10 minutes I think, and the minimum should probably be 5 minutes.
All that said, it seems like you are all set for now. In the future, please post your questions/feedback on the primary thread here: [DEPRECATED] Updated Ecobee Suite, v1.4.0 (Free)
Enjoy!