Do not have much in the way of an explanation but I too have experienced some "inefficiencies" with mail syncing. I am surprised by this because the mail application on my G1 never had these problems.
I am going to go out on a limb and someone else can correct me where I am wrong. I believe some of the application issue with this build of Android are directly related to the fact that we are on a CDMA network. On a GSM network the connection is always available and therefore you do not have the available/unavailable (data connection) that the applications here have to deal with.
For instance, I just recently noticed that when I am connected to a wireless network and the screen turns off (times out) and then I turn the screen back on I can see the wireless re-establish a connection. Now if the mail client is set up to only sync so often and it happens to attempt a sync when the connection is temporarily unavailable it may "miss" and wait until the next check is required.
I was very interested to see how applications would perform in this on again off again data connection environment. As a phone call comes in the data connection is again either killed or deferred until the call is complete (CDMA).
My phone failed to sync one mail account until I restarted the phone then the sync was successful. This led me to believe that the background process was hung and unable to establish/complete the sync. Anyway, something to keep an eye on.
