So, I get home from work, and some friends arrive for dinner. A case of beer (give or take a 6) and they leave. I turn on the monitor, and a ps -ax | grep evol reveals that Evolution is still running even though I x'd out of it last night (as I do every night). There were so many processes, it was faster for me to log out of X and log back in than it was to attempt to kill -9 everthing.
Upon re-login, all of my missing email was there. Apparently x'ing out of Evolution isn't a guarantee. It may still be be running in the background, siliently collecting your email