WOW, now I feel stupid. Yes, I have a clone of my drive. I kinda wondered in the back of my mind why when choosing open with, my external hard drive stars spinning. I made sure to exclude it in spotlight searches but never thought about it suggesting applications twice!
As for the tips at that link... should I do that with the external attached? Would it even help my case where the reason is that I really do have two of each application, just in different locations?