To clarify, it is important to note that the HTML presented above is not necessarily directly related to the search query you’re making.
I would advise disabling any plugins that potentially modify the search query. If that doesn’t remedy the issue, there may be a query filter within your currently active theme or a plugin on your installation that is executing on the search results screens and interfering with the pagination of the query.
If your theme supports displaying the pagination as “next/previous links” instead of a numbered pagination bar, I’d advise turning that on, as that is the WordPress default pagination output.
If the pagination works correctly with that setting on, the issue is then with woo_pagination(), built into the WooFramework. Fortunately, this function has recently been updated and should be far more accurate. If that is the case, I’d recommend updating to the latest version of the WooFramework.
If the pagination doesn’t work with the “next/previous links” output, we can confirm that the issue is a query filter that is interfering.
At that stage, I’d advise contacting WooThemes support directly, where the support ninjas can debug the issue with you directly. They may need to have a more detailed look at the code itself, which is best done one-to-one. 🙂