Permalinks redirection not working

hi there,

Got a big problem..Infact i have created page templates and i have included a hand made plugin, using of course all of wordpress functions. however when i activate the permalinks structure with /%postname%.html, it changes all the permalinks on the website but not the ones that i have made with my ‘plugin’.
i.e

http://www.mysite.com/?=p36 becomes http://www.mysite.com/mysite.html

but

http://mysite.com/mysitecat?article_id=246#articleAnchor stays the same.

Any idea?