The problem was due to insertion of the comments between the the open and close tags
(http://schema2beans.netbeans.org/issues/show_bug.cgi?id=132795)

<TAG>some_comment</TAG>

even if there we no comments, a blank line was added preventing the schema to validate an empty bean.
I have attached a workaround that I have made. Probably It can be done better, but I had problems opening the file in my
IDE (NetBeans).

The patch is for JavaBeanClass.java I will attach it too


*** JavaBeanClass.java  2007-10-03 11:28:10.000000000 +0200
--- /opt/NBSOURCE/schema2beans/dev/src/org/netbeans/modules/schema2beansdev/JavaBeanClass.java  2008-04-14
23:34:44.000000000 +0200
***************
*** 1549,1555 ****
              // Go over the attributes
              for (int i = 0; i < size; i++) {
                  Property a = (Property) attrList.get(i);
!                 if (!a.isAttribute()) {
                      hasSubElements = true;
                      continue;
                  }
--- 1549,1556 ----
              // Go over the attributes
              for (int i = 0; i < size; i++) {
                  Property a = (Property) attrList.get(i);
!                 if (!a.isAttribute() && !"comment".equals(a.dtdName)) {
!                       //System.out.println("SCANTIDEBUG" + a.dtdName );
                      hasSubElements = true;
                      continue;
                  }
***************
*** 3123,3128 ****
--- 3124,3132 ----
      }

      protected void genWriteAttr(Property a, String varName) throws IOException {
+       if("comment".equals(a.dtdName)){
+               return;
+       }
          boolean isScalar = a.isScalar();
          String dtdName = a.dtdName;
          String namespace = a.getNamespace();