Just a little tidbit of info I stumbled across the hard way and wanted to post here just in case any of you run into the same problem. I recently reconfigured all of my WordPress installs (about 9 of them) to be a network. I hope to make a detailed post about that soon enough as it actually went really well. As part of that process, I parked all my domains so they would point to the main network site. Then I killed off all my old subdomains (Bluehost uses subdomains to route addon domains I guess) and databases, just a bunch of cleanup. What I didn’t realize is that during the killing and cleanup, something I did reset all of my MX entries and killed all of my Google Apps Alias email addresses.
It’s no big deal, right? Just populate the MX entries again and good to go. So I did, and much like in the past, sent myself random emails from account to account (all my emails are Aliased, so they all come to my main inbox) to see when the DNS stuff was done. I kept at it for a day. The next day I started going in and tweaking my MX stuff, reading help articles, using MX check tools. It was killing me! I kept working at it all day!
And then… I accidentally clicked on my All Mail box, and there they were. Every single email I’d sent. I Googled this strange behaviour and there it was… email sent from alias to alias/main email does not appear in the main inbox to avoid clutter! Wish I’d seen that sooner or read about that change somewhere as that is how I always tested in the past.