On my "related accounts" tab, I have 4 or 5 accounts showed. But I actually have more than that! I can login to other SE sites which show the same 4 or 5 accounts but not the others.
I have the same openid (google) on all the sites.
In my experience this fixes it 99% of the time.
I'm currently seeing the same issue; I've got multiple accounts on the SE network, and not all of them are listed. But it seems there's just one account missing, so maybe this'll help to track down the problem.
My scenario is as follows:
The one I'm currently not seeing from any of the accounts is http://german.stackexchange.com/ - could that be because the beta phase is not yet 100%?
It's not related to beta in general, because in that case I wouldn't see http://scifi.stackexchange.com/ listed. That one is still in beta too, but Area51 lists it as 100%.
However, if that were the reason, why would it be listed in the "all sites" dropdown?