The overqualified part definitely applies, since they assume that you'll quit as soon as something better opens up. Which, to be fair, is usually true.
Oh I hadn't really thought of that part, but that's a very good point.
I had imagined they'd assume you'd be gunning for a raise in short order or they might not enjoy having an admin assistant who is quite possibly more intelligent than themselves.
On a more "ideal" note, they may also not want someone with a Master's because they feel that their expertise would be more useful elsewhere and that their talent would be wasted in a secretarial role.
