Question about SH404SEF and article links in category view

Take a look to this site : vonnas.com
On the homepage, you have a link to "Voir toutes les actualités" (see all news).
On the category page, you have 3 news.
If you click on the first one, you arrived on the right article.
If you click on the last one, you are send back to the home page but without the article...
If i change the type "Actualités" to Joomla Article View -> Allowed, then the problem is on the 2 first articles.
If i take a look to SH404, Sh404 find for one article 3 differents urls :
index.php?option=com_content&Itemid=101&catid=39&id=109&lang=fr&view=article
index.php?option=com_flexicontent&Itemid=370&cid=39&id=109&lang=fr&view=item
index.php?option=com_flexicontent&Itemid=245&cid=39&id=109&lang=fr&view=item

By default, SH404 put the "com_content" as the regular url and the 2 others as duplicate url.
If i try to create in my frontend slideshow a link to an article, i cannot do it unless i create a link in a menu.
I also see this in my different trying :
If i change the type "Actualités to "redirect", the article is not found (i'm sended back to the homepage) but the url is :
vonnas.com/Actualites-de-Vonnas/renovati...ion-energetique.html
And if i remove the category name to this :
vonnas.com/renovation-des-logements-et-t...ion-energetique.html
then i have the article shown !!

I can always find a way to get the right url but for the others admin of the site, it almost impossible to manage...
What's going on with this ? What did i missed ?
Thanks
Xavier

I have a correct behavior if i deactivate sh404...
For now, i deactivate it : i think there is some more adjustments to do with sh404 and FC3 for now.