well if you look at the last synchronization when you click on your account, you will notice Mail app makes changes every 15 minutes, then it resets and goes back to "last update 1 minute" until 15, so if you make the changes at minute 3, 5, 10 or 14, would be the same, it will make the changes until it goes to 15minutes from last synchronization... yes, even if you set as "as items arrive" or "based on my usage", it's still 15 minutes.
I made a test, sending mails to myself, and it works as expected... you get them immediately it pushes the mail to the mail app, but Mail app doesn't seem to "push" the changes you make to mails and then you have to wait 15 minutes for that.
so your only option it's to do it manually or wait 15 minutes.
so it's not a synching problem per say, it's the way the Mail app is doing it, right or wrong? that's the way it works for now. yes, it must be fixed but not today so we must wait to see if TH2 brings good changes an updates for these small issues.