Hello,
the issues you are mentioning may be related to the problem of prevension of duplicate URLs.
(see
I am experiencing duplicate URLs like -2, -3, etc. Is this an error? What should I do? for reference).
The functionality you mention may be related to the Itemid value. Thus to prevent the unwanted behaviour you may set the "ignore multiple sources" to No in JoomSEF configuration, but then you may experience duplicate URLs. The second option is adjusting the links to articles from the frontpage slider manually. (that means adding them manually with different Itemid value to list of SEF URLs in JoomSEF) -- of course, they will need to have different URL than is that used for "common" dispaly of the article.