In terms of other search engines, Overture offers similar results and Miva has no tracking at all.
Does anyone use/recommend an independent tracking tool that can provide accurate results across all ppc accounts. We have used dc storm in the past, but this cost 10% per click which was far too expensive.
On a side note: Do you track all of your marketing channels and partners through the same tracking solution? If no, they'll never match internal numbers all that closely, I've found. But, this would cause them to over-count, not under-count as in your case...
Beyond this advice, none that I've tried have been all that accurate nor dependable. Especially Atlas One Point. Avoid it. Beyond that, if you find another one that works, PLEASE sticky mail me recommendation. :)