In regard to the issue of rendering at zoom levels that are even (25, 33, 50% etc.) or at 100% only, what version of Photoshop are you using and, if it is CS5 or CS6, have you enabled your compatible graphics processor? Have you tried turning the graphics processor settings on and off to see if the OpenGL rendering is potentially causing an issue?
Another thing to try is to stamp all of the visible layers (CMD-OPT-SHIFT-E [Mac] CTRL-ALT-SHIFT-E [PC]) to burn in all of your adjustment layers into a single layer at the top of the stack and then flatten - see if that makes a difference. You will essentially be flattening everything into a single layer, but it will be a new layer. The subsequent flattening process should not change anything. You could even turn off or delete all of the underlying layers (the adjustments, etc.) and just proceed with your new stamped layer, if the stamped layer appears unchanged.
Another thing to try is to watch the histogram to see if the image flattening is changing the image data (black point, for example), or if the image just appears to be rendered "incorrectly" when you flatten it.
Basically, you want to see if you can figure out whether the image appearance is changing during flattening, or if the actual image data are changing (shifting BP or similar) during flattening compared to the image data as it is represented with the layer stack.