If you have the following directory structure: www.mydomain.com/forum/ www.mydomain.com/helpdesk/ You can not save separate login credentials per directory. Try to save basic authentication login credentials for /forum/ directory and access /helpdesk/ directory with it's own basic authentication panel... you'll be presented with the credentials from /forum/... There may be a server side setting which influences this (realms?) however, the behavior of WebKit/Safari in this instance is presently different from other major browsers.
Form autofill is not part of WebKit, it's in closed source parts of Safari. I'm closing this bug as INVALID per our policy, please report it to Apple via <http://bugreport.apple.com> (free registration required). Sorry that it took so long.