What exposure techniques did you use? I am just guessing you left your camera on auto to handle the lighting transition?
I was on a 2 week trip. Sorry to take so long to reply.
I'm developing a Lua script that sets the exposure parameters over time, using the measured brightness value from the camera. I'll post it when I get it figured out a little better. Leaving the camera on auto doesn't work very well, because the camera adjusts exposure in 1/3 ev steps or larger. This causes "flashes" in a time lapse.
With chdk, you can adjust exposure in 1/96 ev steps, eliminating the flash problem. But the brightness measurement at low light levels, when the stars come out, loses resolution and jumps by around 1/2 ev or so, leading to flash problems if you use it for exposure setting. I'm working on ways to smooth out the brightness changes.