The fact that the question mark is used in the generated urls depends on whether you are using php as an Apache module or as cgi/fastcgi.
In the latter case, eZPublish assumes that your server cannot do rewrite of the incoming urls, so puts the path to the content in the query string.
The fact that some urls get generated with the question mark and some without is very strange - it might happen if you have recently changed your eZPublish configuration and did not clear the caches / regenerate url aliases. By default about the only url that always uses the query string is the one for the search module.
You can check out / try to alter the settings in site.ini in the override dir to get a proper setup: ForceVirtualHost, MatchOrder
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I don't really get it. You say that it depends on the mod_rewrite of apache, so thinking about it, the first installation of ezp was done on a server that has it enabled, then has been moved on a server that it has not. Certainly is not a problem of cache.
In site.ini I didn't override the ForceVirtualHost option, so in the root site.ini is set to false. The same goes for the MatchOrder option, not overridden and set to uri;host;port.
I'm sorted somehow the problem of the login module, but the wrong address generated by the rss module remains. I'm start thinking that it could be a bug.
This topic might be helpful: http://ez.no/developer/forum/install_configuration/possible_to_remove_path_to_ez_index_php_under_fastcgi/re_possible_to_remove_path_to_ez_index_php_u__2