haven't seen this problem. Only suggestions I can think of is look in the database in mp_SiteHosts or mp_SiteFolders depending on what kind of child sites you are using and make sure none of the host or folder mappings are in there more than once with different site ids.

yep, that should be fine so I have no idea why it would return the wrong site. each request it looks up the site id based on the host name, if it is not found then it returns the first siteid which is the default site so any unmapped host names should resolve to the default site but any that are mapped should return the correct site id.