I haven't used blob/clob fields much in the past. But one thing you might be able to do is step in during the ejbLoad() and ejbStore() callback methods. This way, you can handle the large fields and byte arrays.
If you have the 3rd edition O'Reilly book on EJB (the wallaby book), see page 298: Using ejbLoad() and ejbStore() in Container-Managed Persistence.
I am running into this same issue. Did you ever find a resolution for this problem? I am currently using Jboss 2.4.4 and DB2 7.2 with fixpak 5. I have also noticed that as long as you let Jboss persist the original object you can still see the object correctly through the Entity Bean. I gets all screwed up once I cycle Jboss and try to see the object.
Thanks for your assistance