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Hi Steve

I'll jump in here along with Tom about the pixel counts.

There can be several problems for this yet yours is that you are in 16 bit mode with two layers.  It is really strange yet I have seen this.  Let me quote the help file from Adobe about the Pixel Count:

If you read it directly it is not telling you that it will count all of the pixels.  When I have used 16 bit mode under certain circumstances the count is divided in two.  You can easily check this by just temporarily changing to 8 bit mode and see the count double back up.

Here are the other two issues that come along (these are not your primary issue)

- If you are doing a count of pixels of a Layer and the transparent pixels are not absolutely transparent then they will be counted as a full pixel.  I don't know how your are erasing you image pixels yet brushes have partial transparency to worry about.  Erasing in 16 bit mode does not as easily get down to absolute transparency if there is only partial erasure or a feathered brush

- Pixel counts don't always update when you take various actions.  Sometimes the cache level indicator changes indicating you need to refresh yet there are other times when you can be erasing pixels and the count won't change at all.

So bottom line there are several ways you can run into issues yet yours is just that you are using 16 bit mode and getting a half count with the Layers used the way they are (my best guess from experience)

Hope this gives you something to look at.