Yeah it would appear this happens only when sites are created in the back-end sites created on the user side are working fine.
I confirm. Same bug on my WordPress 3.0 multi-site, and same solution. Created in the backend site deliver a wrong wp-admin adress.
Adress created : http://domain.com/subdirectory_mainsite/newsite
wp-admin obtained fot the newsite should be: http://domain.com/subdirectory_mainsite/newsite/wp-admin
Or, when created in the backend, wp-admin obtained become : http://domain.com/subdirectory_mainsite/wp-admin
Which means the superadmin of the main site...
But when I've disconnected myself to create a user and make the same site the user's side, it did perfectly the good way.
Hope this bug will be resolve next version ;-) Maybe somenone should tell this to the developpers, but where ?
Love WordPress 3.0, whatsoever.