Hi,
The menu module not being displayed is most likely caused by incorrect Itemid being stored with the URL for login page. Find out what Itemid is stored with the login page URL (using Manage SEF URLs in JoomSEF) and check if it corresponds to correct menu item (the Itemid in URL is the ID of menu item in Joomla). If it's not, either change it to ID of existing menu item with correct modules displayed, or create a not published menu item, set modules you want to be displayed for it, and use its Itemid.
As regards the 404 warning, are you sure the URL you set for redirect is created in JoomSEF?
Flash not working may be caused by relative URL used in the flash instead of absolute one, which then causes problems with SEF URLs. You can either change URLs to absolute form (with domain) or try changing the "Set page base href" option in JoomSEF's Advanced configuration.