I'm using magiclantern-Nightly.2014Oct07.550D109.zip on my 550D. I've done many timelapses without problems using exactly the same settings and procedure until upgrading to the latest ML. I left my camera doing a three-day timelapse, taking one photo (JPEG) every 40 seconds and plugged into a DC coupler. I set the ISO at 200 (with highlight tone priority), exposure compensation -1.0EV, and the aperture at f/8.0, and partly un-screw the lens to save wear on the aperture blades (which also locks the focus too). I use aperture mode, so that the camera automatically varies the shutter speed as required. (Perhaps I should use exposure ramping but I'm just using auto-exposure for now and blending frames together.)
The intervalometer works as expecting during the day but as soon as it gets dark the exposure behaves strangely: Every second picture appears correctly focused, but the pictures inbetween are very under-exposed (e.g. 4 second shutter speed (according to EXIF) when the normal photo is 20 seconds). The transition shutter speed is about 4 seconds - as soon as a longer shutter speed is used the next photo has a strangely short shutter speed. This lasts all night until the shutter speed falls below 4 seconds at dawn. At the transition point the exposure is only jumping between 4 and 3 seconds, or 4 and 2 seconds.
I cannot find any reason for this to happen, and I believe I am using exactly the same settings as with previous ML versions, and I can't find anything odd in the ML menus. I therefore think this is a bug - somehow the ML intervalometer is messing up exposure settings or shutter speed when it is dark.