I recently rooted my phone, and am using CyanagonMod. But, any time my phone restarts or I have the slightest backup (I think), my phone reverts back to the stock apps. I'm using LauncherPro, Handcent SMS, and Smart KeyboardPro, all of which I've noticed go back to the phone's original apps.
I don't really think it's a root thing or a CyanMod thing. Before then, I had to click the default for Handcent all the time when the app updated.
I can look back at this post from 18 months ago as a newbie and report an update for those that need the advice.
In order to get your whole setup back, you have to restore your 'data', not just the apps. After that, while operating your phone normally for a few days, you will have to set your defaults again. There's no way to avoid having to reset your default apps (as far as I've seen).