I had a similar issue when I did my upgrade from 994i to EISY. Are you using a new PLM in your system? I used a new USB PLM in my scenario and physically flipping any switches or lights on the wall units would not update the IoX status in the admin console.
My fix was creating a new scene and adding the troubled device as a controller to that scene. I then right click on the device on the admin console and restore the device. Once EISY finish writing to the device, I delete the scene. This restored functionality to the device. Repeat this for all your devices that are having issues.
The steps listed above did not worked for the IOlinc garage controller though. I had to remove the device from the system and re-add it for it to work correctly.