Did you double check your permalinks settings in admin panel? And also verify that you have the rewrite rules in your .htaccess file at yoursite.com/.htaccess
Compare the ones in the .zip you downloaded to the one located on your server. If you are missing the rewrite rules you will get a page not found error too.
You should see something like:
Options -MultiViews
<IfModule mod_rewrite.c>
RewriteEngine on
RewriteRule ^articles/{0,1}$ articles.php [QSA,L]
RewriteRule ^articles/entry/([^/.]+)/{0,1}$ articles.php?action=viewarticle&articleUri=$1 [QSA,L]
RewriteRule ^articles/entry/{0,1}$ articles.php?action=viewarticle&articleUri=$1 [QSA,L]
RewriteRule ^articles/category/([^/.]+)/{0,1}$ articles.php?action=viewcategory&articleCatUri=$1 [QSA,L]
More code here....
If you are missing the rewrite rules and any related commands you may need to re-add them or reupload. Usually better to add them manually just in case you have other codes in there like ip blocking, redirects, etc..etc..