I used Java3D a bit awhile back but I don't recall having this problem. When you create your JPanel and JFrame yourself, are you setting everything up the same as the builder, like using the same window style and such? One thing you could try is remove unnecessary settings from your GUIBuilder built panel and frame and see if that helps.
I do not even see a Canvas3D. I thought Java 3D was deadish.
Java3D isn't dead, why I don't know, but a lot of people seem to use it, and Canvas3D is valid, http://java.sun.com/javase/technologies/desktop/java3d/forDevelopers/J3D_1_2_API/j3dapi/javax/media/j3d/Canvas3D.html
Sorry for my English
Your English is fine.