I had a call with the tech team a while ago about this issue when I brought it up, and they fixed it for the queries I was looking at, but there are still many times that the numbers are way off.
I'd write to Google from inside your account and detail exactly what geographic area and queries you're doing that brings up the improper numbers. In the email, ask for it to be forwarded to the AdWords tech dpt as it's a bug in the system and that you don't want the standard 'cut and paste' reply, but instead want the email passed on.