I already had this kind of issue with the internationalization plugin and never got any help, hope I'll be more lucky on that one!
The autonav always breaks up the navigation logic ....
I have 2 menus, one using autonav the other using common links like index.php?cID=1

When I click an autonav link I am taken to a page with a url like index.php/alias-of-a-page/ now if I click a link on the other menu and want to go to index.php?cID=125 I am taken to an odd url with a whole bunch of things added to it like index.php/alias-of-a-page/index.php?cID=121

Maybe with a live example you'll get a better idea !... if you go to elhoster.com/jujuy/index.php , try to click a link from the menu that says "Circuitos" , once you've clicked and get to the wanted page, click on any of the main menu above, apart from the "home" one and you'll see exactly what is happening ...

Hope I can get some help this time ! Many thanks