As Yaya pointed out, it very well may be the cable, as they can go bad, suddenly. Are you using the Phase One wake up, with the button? I will get this message at times on my IQ back, using the Kapture Group cable, but not as many as you mentioned, as that's pretty much a deal breaker for sure. On the rm3di/lens are you using the Arca cable release with the mag attachment? I moved away from this as it just wasn't as accurate as I would have liked, and went to a traditional screw in type.
However as you back just started doing this, did you upgrade firmware? There was some talk over on getdpi, where some older IQ backs, 160 and 180 did not work as well with the Kapture group style cable or the Phase One wake up style. Issue seemed to be dependent on the age of the back (older backs mainly) as a different part was used and tolerances did not work as well.
There is a small tone that is made each time that the back has to hear, and thus sync the shutter, as I understand it, it's a audio type sync. If that becomes non workable, then you will get the message.
If you have not updated firmware recently, I would consider trying a new or different cable. The other test as Yaya mentioned is to try zero latency, just to see if you get any errors, as if you do, then that can point to something in the back, not cable related. Zero L is not a great solution long term as the battery life and heat will tend to get extreme over time.
Paul