Hi,
On Win 2003 by default it is the IIS_WPG user who needs permissions, read permissions for the whole web and full control for /Data and /App_Data
mojoPortal only has 1 Data folder beneath the root of the mojoportal installation so I am confused by your question. Do you have 2 copies of mojoportal installed, 1 in the wwwroot folder and one in wwwroot/yourdomain?
It sounds like it is really running from the wwwroot//yourdomain folder not the wwwroot folder so any /Data folder directly beneath wwwroot is not being used by mojoportal.
Even in a multi site installation there is only 1 Data folder and site specific data is stored under /Data/Sites/[SiteID]/
The Setup page does test file system permissions and indicates if there are problems, /Setup/Default.aspx
So I can only guess you have an extra copy of mojoportal files in the wwwroot folder.
Hope it helps,
Joe