Use seam-gen to create your project and it will work. The problem is that you have to convince your Ant script to use the classes compiled by eclipse, not classes compiled by Ant. The seam-gen Ant build is smart enough to do this.
Yeah, this used to be done by way of the JDTCompilerAdapter, used by the compiler attribute of the Ant javac task. With Java1.5 that adapter barfs on the annotations. I've read that you need to pass compiler params to javac, but apparently that can't be done with Ant 1.6.x. Oh, I got it. It was the Seam Getting Started Guide that requires Ant 1.6.