AFAIK, some stuck pixels can be unlocked by long exposing the sensor. I used myself this method (exposing 3 times 5 minutes) and now CHDK counted "only" 130008 bad pixels from 300000. Hmmm! There is a decrease from 2.5% bad pixels to 1.08%. I wonder what's the maximum limit of bad pixels accepted by the manufacturer?
CHDK only deals with dead pixels that always return a value of 0.
While stuck pixels (that always return a non-zero value) are technically 'bad' we don't cater for them.
A long exposure is more likely to show stuck pixels; but very unlikely to magically fix them.
Did you use a lower ISO the second time you ran the bad pixel detection in CHDK?
More dead pixels will often show using a high ISO.
If you want to use the built in bad pixel interpolation in CHDK (DNG 1.1) with the bad pixel list detected at low ISO, then when you shoot at high ISO you may end up with pixels not being corrected. It's better to use the bad pixel list detected at high ISO - the cleanup code will ignore pixels in image that are not 0 even though they are in the list.
Phil.