Old thread but answered my question...I was also getting the "Bad - Check Installation (0.00%)" notification on a new Davis VP2 Plus w/FARS. My circumstances are exactly as the OP's...ISS mounted and all data flowing as expected with the exception of the anemometer which isn't installed yet.
I just realized the reason why I wasn't getting a "Bad" station comms error initially:
I had the ISS powered up in my study and connected the anemometer cord just to make sure it was functioning properly. And periodically twirled the cups around and rotated the vane. Predictably, no comm errors were noted. The next day, I unplugged the anemometer and moved the ISS to the intended siting area some 350 feet outside the house. Data continued to flow back to the console in fine fashion so I dug a hole, leveled/braced the 4" x 4" x 8' ISS mounting post, filled the hole with concrete and mounted the ISS after the concrete set up.
And then the next time I checked WeatherCat > Tools > Status, I had the same error reported by the OP despite no apparent data transmission problems.
So, glad to hear that error will likely go bye-bye after I get the anemometer mounted/connected sometime in the upcoming week.
Since two of us have written about this, it's likely others will experience the same situation in the future. Might be worth adding a line or two of explanation in the WeatherCat manual the next time it's revised...presumably in conjunction with the upcoming V2 release.