write out the steps you are doing and ill try to see where you went wronge.
So here's what I did;
Using Root Explorer
1. copy com.swype.android.installer-1.apk from data/app to system/app
2. rename com.swype.... to swype.apk
3. in data/app tack on .bak to com.swype.... to make it unreadable
4. reset permissions on swype.apk in system/app
5. reboot
6. after reboot, check that swype is working
7. open Metamorph
8. unzip/extract Black version and Blue version.
9. go to Pick existing theme> SwypeBlack> SwypeBlack.xml> swype.apk sub theme.
10. Everything seems to load fine after about 15-30 seconds.
11. reboot phone
12. check swype. Still works but theme does not apply.
13. repeat steps 9-11 with Blue, achieve same results.
The only thing I can think is that I am using the current legit version obtained from Swype and the last time, I was using the version that was floating around on here for download. Any help would be much appreciated. Always hate it when I hit a moment of Droid Don't, but with this community, that never seems to last long