should be reading 13.4 as 12.6/7 is 100% charged. You must either have a surface charge on them due to charging current
from the alternator
or solar panels
etc. or you are reading them while running your charging equipment
in float mode.
In order to take a proper reading you must turn off ALL charging sources and ALL use sources for 24 hours to allow the surface charge to dissipate. Alternatively, you need to find a battery guy who can put a HD load tester on them.
The LINK if it is working properly is measuring the amp hours left in your batteries...not the voltage.
If you believe the batteries are indeed in good shape and that the link is the problem, the factory reset instructions are on page 22 of the manual which you can access here. http://www.xantrex.com/web/id/76/docserve.aspx
Note that AFTER resetting to factory defaults you will need to go back into the menu to reset the battery capacity to 600ah's for the house bank as 200ah's is the default. It is unlikely that the Peukert exponent setting is responsible for what you are reporting but that should be set properly as well after the re-set.
Note that if you disconnect any of the thin wires from the Link you need to reconnect all in the precise order noted in the manual. You should of course check the condition of all connections as a first step.