Can you test the ND filter manually? Use the CHDK override to set the shutter speed to something like 1/100 and ISO to 100. Set the ND filter "in" and take a shot of at normal room daylighting levels. Then set the ND filter "out" and take a shot at the same light level. Does the brightness change? Then set the ISO in the Canon menu as high as it will go (e.g. 1600) and the scene mode to "fireworks" if possible Then set the CHDK shutter speed override to 1/1000. Point the camera at something really bright (like a 100 watt bulb from 12" away). Test with the ND filter in & out manually.
But eventually, I found a solution that gives me plenty of satisfaction. This is a little bit some kind of patch up monkey business (don't know how to say it in english...), but I found a very simple way to prevent the neutral density filter from engaging: I set the overexposure on +2 Ev (on Canon's Menu). As the camera doesn’t understand that the picture will have a correct exposure, I tell it that I want an overexposed picture, so it blocks the ND filter. It will probably work the same if you want the opposite (-2 Ev to force the ND filter), but I didn’t try it yet. Since that, I’ve done hundreds of pictures and they are all perfect: same settings and good exposure.
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