Enhancement request is made, and now the sound of crickets.
I do not want to trash, smack or smash Solidworks.
See this as a warning if you will, if I myself had come across a post similar to this one I would not have 26 assemblies with 518+ components in each, that I now need to revise.
Solidworks makes it clear in there help file in regards to the limitations of the Hole Alignment tool, but in a software geared torch speed and ease by using tools as Copy, Pattern and Mirroring, it is essential that the tools provided to help you check your design is up for the task.
My example of this is 2 blocks on top of each other where the left holes has been pattern in the X+ direction with 1/8 difference, and the Hole Alignment tool do not recognize it.
I hope this post will help raise a flag so new users do not make the same mistake I did, and if you agree with me, do me a favor and make a enhancement request for this tool to be at Solidworks 2009 standards on the Costumer Portal. Thank you and Sincerely Lars Christensen