This is block to add in your schema:
xs:annotation>
xs:appinfo>
jaxb:globalBindings>
xjc:simple />
/jaxb:globalBindings>
/xs:appinfo>
/xs:annotation>

I had exactly the same problem, and I found the following blogpost:
http://weblogs.java.net/blog/2006/03/03/why-does-jaxb-put-xmlrootelement-sometimes-not-always

The solution is very simple: put the following block in your schema:

and add the following lines to the tag:
xmlns:jaxb=”http://java.sun.com/xml/ns/jaxb”
jaxb:version=”1.0″
xmlns:xjc=”http://java.sun.com/xml/ns/jaxb/xjc”
jaxb:extensionBindingPrefixes=”xjc”

This will force JAXB to generate the @XmlRootElement annotation

I hope this also solves your problem