This is based on this Support Thread: http://devot-ee.com/add-ons/support/zoo-flexible-admin/viewthread/4202
In short: the menu in MSM doesn't change without HARD refreshes every time.
It looks like no one has managed to crack this nut yet and it's partially due to the ExpiresHeader, but I have no idea how to exclude a certain path by the expires header rule or any other way.
Thoughts? Client keeps emailing me saying she can't find things due to switching sites -- irony, since the Flexible Admin is meant to make it easier.