I have exactly the same problem. I received an important mail just two days ago and search doesn't even find it. Flagged mail no longer works either, so it's nigh on impossible for me to find my mails to respond to later. It's accurate to say that to me, in general Mavericks Mail.app is no longer a useful mail tool since it utterly breaks my mark-for-later-response workflow.
What's worse is that this is a massive regression. This all used to work fine. It's somewhat upsetting that I can use my four-year-old Apple laptop to effectively use email and yet my brand new one is useless. With "progress" like this, how can Apple expect brand loyalty?
EDIT: In case any Apple people read this, I am using a Google Apps mail account.
Message was edited by: redpola
I'd like to say that I believe I've completely fixed the problem, by rebuilding my spotlight index.
Open System Preferences
Open Spotlight Prefs
Add your hard drive. You will be prompted "Are you sure?". Click Yes.
Wait ten seconds.
Click your hard drive and click "-" to remove it from the list.
Spotlight will re-index your hard drive, including your Mail, and now Mail in Mail.app will work properly.
How this situation occured is still a mystery to me, but at least now I can use Mail.app again.