When you reboot does it still not work. This happened to me and I just rebooted to fix it... also might have to do with the version you have. I have my APK from an old ROM that I guess it came leaked on and it works all the time.
Floating around on these forums somewhere is a version of Swype that wont need to be fixed. You may consider uninstalling yours and installing this one.
Edit: Didn't realize it was against the rules, I will no longer find it for you. It's out there though.