OK....after doing a little testing, I've found that my troubles with doubles messages coming in, and not receiving MMS seem to be related to third party apps.
I had Handcent and had these troubles. Uninstalled it, ran stock and got all my MMS messages, and no double SMS.
I then installed Chomp SMS, and the problems started again. Uninstalled it.
Heard about a new app called GO SMS, installed it, same problems. Uninstalled it and now back on stock.
I really wish someone would figure out the fix for this because I really NEED to customize the font....in my old age, I have a hard time seeing the little letters on the stock messaging app. The bonus is setting a separate notification tone for certain people. Then I know if I need to grab my phone quickly based on who it is.