When you use stacks and also create new versions of images, Aperture does some interesting things. Versions are grouped together inside a stack if you put them there.

To illustrate this I'm starting with a stack of six simple images:

I make a new version from the K and apply some adjustments to get this:

Creating a new version using Duplicate Version (option V) gives me another version right next to it:

I didn't create that stack, but Aperture has done it for me. And this stack is different -- it has a light gray background inside the dark background. It has grouped the two versions for me. I can drag one of the versions out and have them as separate images if I like:

Duplicating versions that are inside a stack makes a version group inside it. Here I have duplicated the T:

And adding versions to a stack that contains the master or other versions of the master automatically creates a version group inside the stack, so putting all the versions next to each other. It's a little like siblings always wanting to sit next to each other when they are with others. Dragging the two Ks I made above into the stack gives me three Ks together:

And this brings up another way to magically make images vanish. Here is an album that contains just the two blue Ks. I created this when they were outside the stack. See there are (2) items in the album:

When I moved the two Ks into the stack and went to look at the album it showed empty -- but the Album still shows a count of (2):

I am not sure if that is a bug or a feature, but it is an easy way to lose images. There is no way to mark an Album to ignore stack groupings, and this is the result. It's not a filtering thing either. Filtering was set to show unrated or better. I also discovered that by using undo and redo you can get the Album to show the stack pick and not the Album pick.