i have a same problem... and i know why.
my host on windows and uses iis and my service provider rejects instalingl any isapi rewrite component because of performance decrease.


joomla's core sef is nearly works perfectly except 404 on homepage(www.domain.com gives "404 - Component not found" if i write www.domain.com/index.php homepage opens)... and just on it. other links works perfectly. same whit sh404sef...

whit joomsef:
no problem on homepage and unsupported extensions. i think joomla's core sef works on unsupported extensions because they have index.php/ and they works.
urls that joomsef's created (urls whitout index.php) gives 404.
if i costumize joomsef's onw created urls ( add index.php/ ) browser gives endless cycle error...

i must resolve sef problem... :( any solution?