"Empty" images in my library

Having a huge library of both JPGs (and their RAW equivelants -I have my digital SLR set to shoot both RAW and JPG simultaneously) I decided it was time to split up my library into two: a JPG-only library for normal use, and a separate RAW library for those times when I need to access the RAW equivelants.
I've been using "iPhoto buddy" to create several libraries on my Mac, so what I did was make a copy in the Finder of that RAW/JPG library, resulting in two identical (large) libraries. I renamed them ("JPG" and "RAW") to easier distinguish them from each other, then added them to iPhoto buddy where I started the one named "RAW".
Using the "smart-album" ability of iPhoto I filtered out the JPG images, then erased them and emptied the trash. That should leave me only with the Canon RAW (.CR2) files.
Well, I do have all my RAWs, but I also have loads of "ghost" images. That is, lots of empty picture frames with the JPG file-names and previously applied keywords.
I've tried starting iPhoto while holding down ALT-COMMAND, then rebuilding/cleaning up things using those 4 options you get, but this hasn't seemed to solve my problems. iPhoto also runs extremely slow, and I see that beachball all the time. Now and then it even crashes as I exit iPhoto with the library etc. Frustrating.
I was curious to see what was contained inside the library's internal folders, and was surprised to see lots of JPG images. In another thread I was told that JPGs were automatically created for each RAW file as iPhoto isn't equipped to display the RAW format(s). But if I double-click them from the Finder I'm told that they're corrupted or in a format the computer can't read.
Looking a bit closer I see that all of those JPGs are sized at zero bytes!
So what has gone wrong and how do I fix this?

I too am confused by the "filing" of iPhoto. I frankly find PC at work easier to organize files. My frustration is I put my Library photos into folers and when I delete them fro the Library, they are also deleted from the folder! How do you organize photos so you can find them and how do you stop eating up memory. I see there are no answers yet.

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