I think this might be the issue connected with Itemids JoomSEF has stored with the appropriate URLs for the news articles.
Check for some details at
http://www.artio.net/en/product-faq/joomsef-faqs#faq5.
You may therefore need to do some experiementing about the Itemid -related settings of JoomSEF.
Try to switch "Ignore multiple sources" to NO. I would do it just temporarily to see, if it will solve the problem. If it does, then it is possible you may need to find, what Itemid should be used with the URL of the news articles.