Archive links don’t work / wrong links generated by php

My blog got hacked by the fake malware warning thing and I finally figured out how to fix that … then upgraded my WP to newest version … automatic method .. and then noticed that the sidebar links to year and month archives fails to work.

The links go to (for example)
http://www.mysite.org/wp/2010/04/

I have another functional blog that has links generated in the following format:
http://www.mysite.org/wp/?m=201004

What I cannot figure out is which php file generates the sidebar links to the archived conent (need to point correctly to year and month). Obviously the second example above is what I need for both blogs.
Does anyone know which file needs to be fixed?