Well, CRM's organization URLs aren't like typical folder structure you would see. (there aren't subsites in the folder structure) .
so the main problem is that when you access one org (or try to) you "sometimes" get a different one? Is there any consistency to the behavior? for instance:
- when it doesn't go to the right place, does it always go to the "first" org?
- is this consistent for all the users? are all the users in all the orgs? ( for instance, if user 1 is only in org1, but tries to go to org2, what happens)(vice versa?)