Your assumption was right, thats the way it works whichever IP is configured first will be used as the Primary VPN peer. In case if its not available then it would fall back to the secondary IP.
In case if you are seeing the connection is always building up with the secondary IP that means problem is at the other end and i am pretty sure if you run the following debugs " debug cry isa 125", "debug cry ipsec 125" it will show you that he is trying to build the tunnel with the primary IP first and when getting no response it is falling back to the secondary One. Make sure whatever IP you have configured as primary is also a primary IP at the remote end.
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We have configured the outside and inside Interface with official ipv6 adresses, set a default route on outside Interface to our router, we also have definied a rule , which also gets hits, to permit tcp from inside Interface to any6.
In Syslog I also se...