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Well a couple hundred thousand ads is quite alot and depending on your server this could take a while. I would suggest you edit your pp-inc.php file and set $showsqldebug variable to show the query timing.
You can then see your query times but more than likely you would need to update your server with a better processor memory or if a hosting environment go to a higher level if your using that many ads. Searching hundreds of thousands of ads depending on your server config settings might tax things. Are you expiring outdated ads? Given the nature of a classifieds site and the temporary content of the site it brings to question also the amount of traffic on the site which would also slow it down.
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