Thanks James, for your input.
I just finished up fixing this. Actually, I noticed the data which existed before I start my Glassfish, doesn't have any issue in loading. But when I persist some fresh entities, and try to load that along with all its eager fetch associations. The associations were being picked up from cache, I believe. Because problem doesn't persist after I restart the Glassfish, and invoke my bean. For fresh entities its always the same, not getting loaded.
Since, my actual query is FOR UPDATE, that really picks all the records from database, but its associations are get loaded from cache if found. So, I tried to use TopLinkQueryHints.REFRESH=true, and TopLinkQueryHints.REFRESH_CASCADE=CascadePolicy.CascadeAllParts. That didn't work, no idea why. It should, IMO.
Now the fix. I manually called `em.referesh()` on that particular entity, which was being picked up from cache. That solved my issue. Below is the modified method,