When Phone Restarts, Stock Apps Revert

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.

Is there anyway to avoid this?

Thank you.