While Searching on line ... I came up with this. I've seen several posts very similar on several boards. It seems that the Apple launcher cares about 32 bit or 64 bit ....
This is part of a change to the double-clickable app launching policy (which we explained in detail in the developer preview release notes). To enabled the Finder's "Run in 32-bit mode" checkbox for Java apps, and to make the transition to 64-bit by default easier, we've modified the JavaApplicationLauncher.framework to only launch application's in the architectures they have present in their JavaApplicationStub.
This was done now for a variety of reasons: until Update 4, the JavaApplicationStub and all apps that were bundled with it were 32-bit Universal. Very few apps required 1.6 in their Info.plist, so now was the best time to switch this policy. Applications with PPC or PPC/i386 stubs would continue to run in 32-bit mode indefinitely, until they rebundled after Update 4, which would then opt them into launching 64- bit (with the ability to downshift to 32-bit using the checkbox Finder's Get Info window). This simplifies the rule down to "if you don't have the architecture present, we won't launch you in it", which is exactly the same rule for launching native Cocoa apps.
The thinking is that if you haven't rebundled, you likely haven't ever considered that you'd be run in 64-bit mode (and when users have dragged Java SE 6 to the top of their Java Preferences, they found that some of their applications stopped working). By preventing apps from being launched in 64-bit if they haven't rebundled, we can maintain the widest compatibility, with a minor impact on developers (and actually let them have a say in what their version and architecture requirements are).
In your case, since you are manually modifying the Info.plist to 1.6+, replacing the JavaApplicationStub is also required, since IntelliJ 7 was likely not expecting to be launched in 64-bit, and may contain some 32-bit only native libraries.
Hope this explains what you are seeing,
Mike Swingler
Java Runtime Engineer
Apple Inc.
Hope this helps ...
Xenon