I have seen this issue and just can't seem to find the solution and it may be something obvious that I am missing.
if logged into WordPress and looking at one of the additional sites, clicking Edit Page in the WP header results in this error. WordPress is installed in the root so I am confused a little by the error. Possibly unrelated to this, clicking My Sites results in the same error, and checking the link for Network Admin it goes to http://www.maindomain.comwp-admin/network/ (notice the missing / after .com). Doing this all from the primary domain however seems to work without any troubles.
Any ideas?