Hello,

it's difficult to say what could be exectly the problem, if links are working the reason could be that the analyzer is in some way blocked on server receiving http status code 409 instead of 200 or 301.

A quick test could be disable sh404sef just to ensure that this is not involved.
Then ensure that in the htaccess there are no directives that could block with the analyzer or other system such as firewalls, etc
Finally the analyzer acts as a crawler thus needing to open socket connections on the server, check if this is supported.

Greetings,

John