blending layers changing response after flattening the layers

I'm using Photoshop 7 to handle forensic examinations of documents, performing blending techniques to enhance variation in tonality, but after joining the layers for printing I receive a different response then when the layers are not combined. I find that the digital file becomes darker with more contrast then before the flattening. Any idea what I am missing?

Thanks for any comment that puts me in the right direction.

One thing that comes to mind is grain.
If your pictures are grainy and you're not viewing them at 100%, the monitor interpolates the best it can and the results of what you see are unpredictable.

Do a "command+0", than flatten to see the real effect.

(command-option-0?)

Also make sure when flattening blend modes that you have a plain white background, and not transparency.

And as an alternative to flattening, try making an empty layer and copy-merging all existing layers into it. Sometimes (only sometimes) this yields are more faithful "flattened" rendition than the flatten layers command.