OK, so to answer a couple of question first:
We are in NX6 native, no PLM. The older components only appear to load at the top line assembly, in this case, a drawing file. I believe we have the "Load Latest" turned off via the Part Version settings being off in the customer defaults so that we can control what UG loads. This is to control drawings revisions better, because there are times we don't want all of the latest parts. It's a timing thing.
The perplexing thing is that the assembly structure was manually updated either by replace components or cloning or a combination of both, so the old components/assemblies should have been fixed or updated.
Ben, even though I understand what you are saying about search paths and alphabetical versus created, I'm not sure what impact that has on my situation. I could understand if the parts were supposed to be part of the structure, but they were not. It's almost like the top line assembly is carrying these "tags" along somehow that are not supposed to be there anymore.
And John, even though I appreciate your input, we almost exclusively use Reference Sets at every level to control component staging and to cut down on the number of entities that come along for the ride at the upper levels. Trust me, with the size of our files, this is a must. We have been doing this for years with little or no problems, so we can't just up and do a 180 now without a lot of grief. I am also not sure how that could affect my situation?
Now for the interesting part! I tried just about everything I could think of when I noticed it seemed like the parts were only loading at the top level. So, I opened the assembly below it first, turned load options to "Structure Only", "Partial Loading" and "Load Parents-->None", then opened the drawing file above it. I noticed it didn't seem to load the old parts, so I did a part cleanup and saved the top level. I closed out everything, reset my load options back to All Components, Load Interpart and All Levels and re-opened the drawing file again, and WALLA! no old components. Now explain that?
Thanks you all for your input and help, but this is obviously a real teaser to look into.