I really don't think there is any way an 'M' flagged account can be denied access to site commands... Try a 'site myinfo' to see the details for the currently logged in user and verify the 'M' exists. It is true that the modification or creation of other 'M' flagged accounts can be denied unless connected via 127.0.0.1 as a security measure but you would get a different error message in that case.
The biggest suggestion I have it to look at the logs directory. Rejected logins will be explained in the error.log file. The most likely causes are a bad .vfs file entry for the root directory (/) or a bad hostmask.
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