I suggest that you carefully compare the "bugs fixed" sections of the respective release notes for the respective versions.
Note that the release date for the 1.4.2_06 version is 2004-12-10 (according to the release notes), while the IBM version name is "20090307" which implies that it was built ~5 years later. While there is no guarantee that the IBM version has tracked all of the fixes to that date, it is a fair assumption that they will have (at least) tracked the security-related patches.
Reason why I posted this because when I tried to do some deployment to server from command line, I am having few issues so wonder this could be difference in java versions.
Possibly, but (IMO) it is more likely that the problem is nothing to do with the version of Java. Either way, I think that an enumeration of the differences is unlikely to help you isolate your problem.
I suggest that you ask a new Question in which you describe your actual problems. We may or may not be able to help ... but I think your chance of success is greater than with your current approach.