problem after upgrade

I have a problem after an extended upgrade process. We had a 2.5 installation that got compromised. Someone was able to insert hidden spam links in several articles.

We made a copy of the database and reinstalled version 2.5. Then we removed the links from the articles and then we upgraded to version 2.5.1.

While the articles will show as one long list we get a “page not found” error whenever the title of an article is clicked. We entered a test article and the same thing happens.

Any ideas how to fix this?

Thanks for any suggestions