Nimo,
1) you worked on the project in Eclipse 3.4/JBT 3.0 (created via "seam create-project" command) and then iported it to Eclipse 3.5/JBT 3.1, correct?
2) Could you try to create a new project and import it in JBT 3.1. using seam-gen (seam create-project). Can you reproduce the issue for such project?