Hells Bells,
I shot for three days with 4.1 DB - no probs - and now today, when I start shooting, I have the same problem as well!
Grrrrr!
EDIT: The only connection I can make, and it may not be significant, is that it started showing this error after I put the mirror up, but forgot to turn off the AF.
The only good news is that the camera / back still works with 3.7.8
FURTHER TESTING: After shooting a frame tethered with 3.7.8, the camera / back starts working again with 4.1 (after 3.7.8 was closed). Works irrespective of whether captured from button on computer, shutter release on camera, and whether or not MF / AF is selected on either lens or focus selection on camera, and whether I try mirror up with AF 'accidentally' left on.
Conclusion: 4.1 is messing with settings on back, or not supplying confirmation to back that it has successfully captured, or some data of that type, hence completing the capture cycle.
Can Phase One do anything right (apart from low noise / iso, long exposure)?
Hope this helps. Get a move on Phase!