Don't see a link to your site, but did you attempt to select your desired permalink structure from the admin area and then save it? Go to:
Settings > Permalinks > Select your desired permalink structure and save it. Do this even if you already have since something may have interfered with your saved selection.
If that does not fix your permalinks, you may have an issue from a problematic plugin and/or your template. To determine where the problem is coming from disable all your plugins until you determine which one is causing the problem. Also, revert back to the default WP theme and see if that fixes it, if it's a theme issue.