I'm curious --
is the display relatively taller on a flat panel versus a CRT?
1280x1024 has an aspect ratio of 5:4 ( 5 *256 == 1280, 4 * 256 == 1024).
On a CRT, that means the pixels will be taller than they are wide.
Is your flatpanel display actually 5:4 in aspect ratio, so that the pixels are still square?