Well it should be easy as the plugin i understand simplifies things alot.
Do you have any .htaccess files on the other non index pages?
If you use firebug is there any js errors on the page that could be tripping up piwik on those pages that dont show?
The titles and sub pages are you sure they are being defined as true sub pages and not just articles off the main page?(again firebug would help see which variables are being fired, page title) I am guessing as you mentioned you get long urls maybe its an issue on how the urls are being defined? Im not very versed in joomla but your description makes me guess something like that…