Yesterday a group of us went out to our dorm repeater sites and upgraded a Bullet from v1 to v2. We had some issues with stability but a power reset fixed the issue. We also installed a second Bullet with v2 on a nearby dorm that sits a few feet higher. The taller dorm called Guinn has a better line of sight, but the shorter dorm was used for testing it is called Stark. 

We maintained both for testing purposes to see the range differences between the dorms. You see we have free roam of the shorter dorm but have limited use on Guinn.

Now for the issue we are experiencing. Using a Rocket M2 on version 1 firmware I had a beautiful signal strength using dual 6dBi Cradlepoint antennas. This is from a hill top, radio sitting in the dash of the windshield facing the Stark dorm. My connection was showing a strong 83% and the air mile distance was 6.5. 

After upgrading all devices to v2, I can no longer see a connection at that distance with the same setup, I've experimented with different antennas to no avail. We did bring a Nano Beam out and managed to get a connection but we could only see one local neighbor and the other devices as remote neighbors. I tested the Rocket much closer in fact on the roof tops of the two dorms and had connections but no where else. 

I am completely baffled, any thoughts that might help explain my issue? 

Thanks!

You don't specify what the RF level was at the car based node for receive ( it's possible To have a high LQ even though you have a weak signal --- it is also possible some other RF device came up and knocked the signal out by being local interference)

6dbi antennas inside a car at 6miles sounds like it would be at the extreme edge of RF range and that this could be a simple as atmospheric changes.