I tried it with http (login to KERIO mailserver), but it did not work in this case.
Fortigate tries to fill the form via some very smart javascript in the browser. This is a generic approach, but probably not ideal for forms containing javascript themselves, I assume.
My own approach was to write a small php script that submits http GET variables via POST, so that I could put the credentials in the URL string (as a dirty workaround).
Sadly, the problem here is that the fortigate currently seems to dislike bookmarks containing get-variables such as http://server/postget.php?username=xxx.
Edit: I filed a bug report at Fortinet, they are working on it.
Though, my workaround should not be used for variables containing actual passwords, because despite the tunnel, in the URL all GET variables go over the net unecrypted, methinks!!
/Edit.
The SSO feature is brand new, so I am sure we can expect improvements here.
Still, I am more curious about SSO for CIFS.
(I do have a nasty workaround for http, for few users...)