the_category acting strangely with query_posts

Hello,
I have been setting up a theme based on one I made in the past. I’ve been having trouble with using the the_category() function. It gives the name of the category the post just fine, but when I click on it it doesn’t bring up posts filtered by the category name. I have disabled the plugins that were activated, but that didn’t change anything. I have been attempting to query the 5 recent posts, which when I comment that out it seems to fix the trouble with the_category() function. I’ve tried a couple ways of querying the recent 5 posts:

query_posts('posts_per_page=5');

The other way I’ve tried is using this before the loop:

$temp = $wp_query;
 $wp_query = null;
 $wp_query = new WP_Query();
 $wp_query->query('showposts=5' . '&paged=' . $paged);

then after the loop I have

$wp_query = null;
$wp_query = $temp;

to fix what that changed before. I didn’t have this issue before while querying a specific amount of posts in the past and I’m not sure which is the best to still be able to get the most recent posts and still have the_category() function still work the same. Just seeing if anyone can give me some insight to what I might have done in correctly.

Thanks!

-Frank