Photoshop CS4 auto flattening my files. Anyone else experienced this?

Photoshop has started flattening my files, seemingly at random. Obviously I don't need to explain that this is killing my workflow and is an unacceptable bug! I am currently reconstructing a 300 + layer brochure file from scratch, which is a real blast.
I have spent a while searching for other people who have experienced this / possible solutions, but have come up with nothing. So, has anyone else experienced this, and does anyone have any potential solutions?
If it makes any difference, I have been running GridIron Flow. I didn't have these issues before installing the app. I have since uninstalled it.
Thanks very much in advance,
Fred

Never work on an original.
Sounds like you are converting your files from RGB to CMYK in the advanced dialog uncheck flatten image to preserve appearance

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