From the CLI you can run the following command to follow the call flow:
debug voice switchboard
From here you can see how the calls are being routed. Possible causes could be max number of inbound calls is set to low and the second call is following a coverage route. Having the main number set up as a DID or alias on more then just the AA. I usually assign the main number to a Ring Group then set that Ring Group up with call coverage going to the main AA instead of a user, this way you can setup different call coverages for Day, Night and Override modes and it can be easily changed in the future. SO if the customer wants a different AA later you can build it out have them record the message and then test it by dialing the AA extension from a handset and when they are happy with it you just change the coverage extension in the Ring Group.