I also had the same problem with Eclipse, and I know from other developers
that they are getting the same problem.
Even more, if you create a sample RCP application from the wizards, and
declare the default intro page (org.eclipse.platform), and export it using
the product export wizard, then you'll see that the intro page always
appear! And is a project very, very simple.
Now, I took a look and examined the code of the openIntro method and it
seems that the error is that Eclipse is not able to save the API prefs in
the PrefUtils.saveAPIPrefs() call. There is no other possibility.
To fix this, I created my own check mechanism with my own preferences
file, and all worked fine. But the bug is there yet.