We have fixed a number of bugs in this area for the upcoming 10.1 release. I'm not sure if the read only setting would have affected this setting, but we'll check that too.
Could you tell us the structure of your application? Is it one EAR with several web / ejb modules? Do you have Java modules too?
1) Restore the project to their original states from clearcase.
2) Instead of enhancing the EAR directly, please enhance each module project one at a time so that we know which of the projects is causing the problem. Finally, enhance the EAR.
3) For the problematic project, can you send us the .project, .classpath and all the files in the .settings folder? This will help us replicate and examine the issue internally.
On the DB connection, can you please clarify exactly what wizard (in RAD) you use to add the connection to the project? This will not affect the enhancement process, however.