The software simply wants to have both off. If they are not off it will ask you to take them off. I have had my firmware upgrade go sour on more than 1 occassion after that which is why I advice you to do so beforehand.
Hmmm... it does state now in the read-me for the 081222 version to leave them on. I am still used to flexcolor where you should take them off, as a matter of being used to that I always do so.
From the readme..
Procedures for updating capture unit firmware via Phocus:
1. Unzip the downloaded file.
2. Make sure your camera is turned on.
3. Connect your complete camera, inclusive the capture unit, lens and viewfinder to Phocus.
3. Go to "File" and then "Update Firmware" and locate the desired firmware package (.cim) on your computer, and click "Update".
4. Follow the instructions provided from the software carefully! Do not switch off the camera during the update process, unless specifically requested by the Phocus software.
5. When the update has been finalized, please check that the firmware has been updated and that your equipment works ok.
Try again with the firmware that did work before doing something else. I have both the R249 & 081222 on my setup disk and I am not sure but one of them did not work. I see on the Hasselblad site you can now only get R251 & 081222. Try R251, the other is combined body & back.
Another option that you can do is the following. Download flexcolor 4.8.6. It will also have a firmware in it (R245). Most definitely an older version. Install flexcolor, it will ask you whether you want to update the firmware, it will warn you that you will be putting an older version in. Do so.
Try again with the newer firmware after that.
You have to be a bit patient and try. I have had firmware screw-ups more than once even to the point of totally bricking the body or at least it seemed that way. Even that is fixable but I have to dig pretty deep in my memory and archive to find how to do that but at this moment you are not yet at that point I believe. The first time can be disconcerting but after that you start realizing most stuff is user fixable.