LR doesn't "see" certain images

This question grows out of a long discussion about file numbering and renaming issues that I previously posted. Having slogged through those issues and beaten them into relative submission with the amazing help of Ed Macke and others, I've ended up with a new issue.
LR (2.4) says that my Master Catalog contains 13264 photos. When I highlight that line, LR says it is displaying only 13224 photos. I have synced the entire catalog a number of times and there now no photos are reported as new and needing to be imported, or missing. I see no ?'s on images.
My setup is as follows on my Mac OS X 10.5.7 with external HD dedicated to back up:
On my HD, in my Mac home folder, I have a LR folder which has 3 subfolders (working catalogs, working exports and working originals). Working Originals in where I keep my images. Working Originals contains 20 + folders. Those folders have no subfolders. For all but 2 of them LR "sees" all the images each contains. Of course, the 2 with problems are very large. One is named "2008 Morocco" where LR does not "see" 39 images and one is named "2008 General" where LR does not "see" 1(one) image. I have separated synced those specific folders... nothing changes.
I have no idea what is going on here I have no idea how to resolve this . All ideas and thoughts are welcome!
thanks!
Stephanie

Oops! Thought I was clear....
What I was asking was why stacking would result in LR's not seeing any but the top of the stacked images.
If, among other things, it causes the type of confusion I just spent so much time trying to resolve, what are the pluses of stacking? Are there other
negatives?
Thanks
Stephanie

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