hi, this thread is one year old but I encounter the same problem and get a solution...
I edited persistent.xml file (throw the editor of netbeans) and sudently my tables wouln't update neither create (jboss 4.2.1.GA, jdk 1.5, mysql).
The guilty line was :
<exclude-unlisted-classes>false</exclude-unlisted-classes>
Setting true or false does nothing, ear deploy, no error message, but no sql neither.
Simply remove this line, now the schema update as suppose to.
A+