Preview of some flattened TIFFs show only one of the original layers

When I flatten the files that I have been working on into TIFFs for delivery to clients, sometimes the preview (or thumb nail) shows only a single layer of the original layered file that I was working with. When the file is opened in photoshop, the complete image is there. Is this a bug or is there a way to correct this before I flatten the image? Btw, I have seen this same issue through many versions of photoshop... from CS3 through CS6. When saving the same flattened image as a JPG, the preview saves correctly.

[This is a rewritten post because I posted some garbage first time. ]
I was pretty sure you were going to say OS X.
Is there an alpha channel (possibly used to store a selection) in the problem files?
On a Mac, if there's exactly one alpha channel in a TIFF, the system interprets that alpha channel as transparency when it generates a preview. And if there's more than one alpha channel then the preview sometimes will be weirdly coloured.
Save As TIFF has a checkbox for inclusion of alpha channels, so clear that when exporting your flattened TIFF.

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