I have a vanilla setup of Sharepoint 2007. A few subsites are also created. When the SOAP API is used to access the base Sharepoint site (for eg. http://spserver.com) the list of subsites and other lists can be retrieved.
When we try to retrieve the data for a subsite using the subsite URL (for eg. http://spserver.com/site1) the webservice returns the data for the main site instead of the subsite.
This is happening when the site is accessed from multiple applications using the SOAP API so the issue is probably a configuration issue on the server.