I suggest that you carefully compare the bug fix sections of the corresponding release notes for the corresponding versions.
Please note that the release date for version 1.4.2_06 is 2004-12-10 (in accordance with the release notes), and the IBM version name is "20090307", which means that it was created 5 years later. Although there is no guarantee that the IBM version has checked all the fixes before this date, it is a fair assumption that they will (at least) keep track of security fixes.
The reason why I posted this is because when I tried to do some deployment on the server from the command line, I had several problems, so be surprised that this might be the difference in Java versions.
Perhaps, but (IMO) is more likely that the problem has nothing to do with the Java version. In any case, I think listing the differences is unlikely to help isolate your problem.
I suggest you ask a new question in which you describe your current problems. We may or may not help ... but I think your chances of success are greater than with your current approach.
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