Hi,
I tried raising offset all the way to 500 (gain still 210) which definitely lifted the range off the left edge for the shorter exposure, but some pixels of the longer one still clip. So the main issue that longer exposures have lower ADU values still remains, even the maximum values, it looks like around 400-500 ADUs have been subtracted from the longer exposure, which causes the low end to clip:
0.01s exposure has minimum value of 176, median 2517 and maximum 6475
1s exposure has minimum value of 4 still, median 1936 and maximum 6015
Both images have similar three peak histogram shapes, but 1s exposure has them at lower values. The fits files are again at http://s2.org/~jpaana/Light3.zip