I may have just forgotten how these Remotelincs are supposed to work. My old Remotelinc and new Remotelinc 2 work, but when I update scenes, both of them give me the 'Cannot communicate with .....' error and I get the red exclamation mark next to the Remotelinc objects in my lighting. But as soon as I actually use the remotelinc, it works fine and the red exclamation marks go away.
I did upgrade to the 3.1.10 beta firmware, but I didn't think this was related to the firmware, so I posted it here.
(To be honest, I'm confused about what the ISY is actually writing to, when the my lighting shows 'Writing' next to the remotelinc buttons just before the Cannot communicate error. It is my understanding that communications are one way from the remotelincs?)