I am having a similar problem (also using JB7/Protegra) but perhaps we can be of help to one another. I have no trouble getting many-to-many relationships working, but one-to-many relationships cause queries to be generated that have column names that don't exist in my database and I can't find where to change those incorrect field names.
One possible workaround is to change my database to have the strange names created by JB7/Protegra/JBoss - but that may not work for you.
Did you get anywhere in your search?
I have verified that the problem is caused by the jbosscmp-jdbc.xml that is generated by JBuilder/Protegra. Fixing that along the lines shown in the Flashline documentation (adding the <key-field> tags) appears to eliminate the problem. At least in my case.
Good luck all!