James, the screen stretch function is just that - a screen stretch. It is by no means the best method in judging the accuracy of a flat. FITS files are numerical. When processing data, it helps to understand the figures.
In MaximDL, on the status bar to the lower right you'll find an item 'I: xx,xxx'. Where ever the mouse pointer hovers on the image, the 'I' value (Intensity) displays the pixel's numerical value. Towards the center of the flat you should be hitting the target ADU. +/- 1,000 isn't an issue btw, doesn't need to be dead on.
If you want to get truly analytical on the flats, use MaximDL's line tool and draw a diagonal line across the frame. This will present a graph showing values along the line. There are a few other ways to make an assessment.
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