Thanks for noticing this, OlRivrRat and Dfort. Obviously, it is a bug on the 100D but there are still much better ways of shooting time lapses that will also provide better results in terms of quality - no desqueezing (and quality loss) required in post. Here is what I usually do:
1) In the Photo mode, with the Silent module, Intervalometer and Life View active. This is the old classical "gradient" way that has been working for years. It provides time lapse sequences in the full sensor resolution, also called FRSP. With the Canon preview set to Hold, you can take a test frame to check focus, exposure and composition and make corrections if necessary. When you are ready, you change the preview to Off and start the actual time lapse. Caveat: At certain intervalometer settings, the time lapse may look a little choppy since there is some dead time between frames.
2) In the Movie mode and FPS override set to some small vallue, say 1 fps. Metering and focusing in this mode is a pain - it takes too long the camera to respond, but once you have the settings right, the timelapse looks very smooth and quality is gorgeous! Caveat: Maximum resolution on the 100D is limited to 2520x1080, (at 5x magnification).
These two ways require some practice and experimenting which is also valid for every ML function, but once you get used to them, the results are really rewarding and well worth the effort.