It looks to me like you may only have both HT chains enabled on ONE SXT.
Check the settings carefully and make sure both chain 0 and chain 1 are checked for tx/rx on both SXT's in the "HT" Tab.
Also, do not trust NV2 CCQ % Unless the link has matured and is under load, what i mean is allow the link to have some uptime, and some traffic over the interface for a period of time (10 minutes for example) otherwise the numbers mean nothing.
NV2 only starts to report a decently reliable CCQ under load, from what i have noticed in my testing.
As others have stated you have obstruction in your path, or mis-alignment of antennas.
With one chain at -90 DBM, you are basically operating in single chain mode.