All posts show in wrong categories

Hi,
The site was working fine but it seems after the last WP update, any of the categories fetches all the posts instead of only those assigned to it. I currently have WP 3.8.2 and Pinboard 1.0.6. Do you think this issue with the posts being out of whack might be fixed by updating the theme? Could you help me fix this issue without having to redo all my php and css changes of the theme? I will pay you for your time.

I am not certain this is caused by a WP update but the timing since the issue began seems to point in that direction.

Thanks!