There may be a lot of underlying reasons for that, petty as they may be.
For example, if a student studied since the beginning with Shihan 'A' and before reaching Shodan, moved (city, town or even country) because of an opportunity (work, marraige partner interest etc..) and while there for an extended time trained and tested for Shodan there with Shihan 'B' - Both Shihans belonging to Aikikai... then returns 'home' and presents the certificate to the original Shihan for recognition... there is a chance that this original Shihan make take offense that the student simply took his Shodan exam with a different Shihan for a number of reasons. Maybe the two Shihan dislike each other... who knows. It may simply be a hard pill to swallow. I can see this from so many bad movie plots "I invested years into your training and then you go and do your Shodan with someone else?"
Not the case here, they were shodan before they ever left, all in one place. After they moved to the new city and the new dojo the retest was required.
Anyway, it's just and example of how things fall through the cracks since there's no real regulation.
Within the Aikikai (or any organization) a rank issued by them 'should' apply throughout anyone associated with the orginization. This is why they issue the passports as a means of convenience for those that wish to intermix with other dojo inside the Aikikai (and in some cases out of it) as a means of common recognition of their rank via the issuing source.
Actually, recognition of Aikikai rank issued by another dojo or organization is required
by the international regulations. The problem being, if someone (especially someone of substance) chooses to ignore them there is no real avenue for appeal.
Petty, I know, but...fair is fair.