- I have to set Input Method back to SwiftKey
- I have to set what application I'd like to use when I clicked sms icon (I'm using ChompSMS)
All these happens after a phone reboot.
Do you have either app moved to the SD card (using Froyo)?
If yes, then you need to move then back. The apps aren't loading when the phone boots, so the phone is reverting to what is currently available on boot (stock SMS/keyboard).
You have to remember: with Cyanogenmod, it will let you move any app to SD card, regardless of whether the app is set to allow you or not. I made a similar mistake with Swype.