I've noticed the autoguide bin settings are set back to 1x1 each time I start Ekos. I change it to 2x2, it runs that way for the sesssion, but the setting does not persist across app restarts.
I'm using an SX Ultrastar. Ekos is the latest git pull as of 29 March 2019.
When you start Ekos you get a popup with configuration options. Open the tab for your guide cam and then the Image Settings tab. Set binning to 2 there for both X and Y. Then go to the options tab and click Save.