Ahaa! But how do you know that it is the iRex version that opens? Have you tried to use any of the features offered by the new versions? They will look like the original ipdf when you open a pdf. Here are some links to the original posts by the people who created these versions. I think you should be able to see how to activate each of the features by reading these posts:
Let me know folks if I've got any of the attributions wrong. I should probably add something about these to the bundle of installers.