I've got a couple of projects that use lists very specifically, and something funky happens whenever the project is loaded:

1. On my Defender II game, a script shows a list, THEN sends the thumbnail graphic to the front. When the project reloads, the list is in front, which really annoys me. http://scratch.mit.edu/projects/10700190/
2. On my newest project, I experimented with rendering in text. Problem is, when the project is loaded, the list changes its location and size, which completely messes up the careful alignment with the center of the stage and the size ratio of the text. In other words, it causes the text to “smoosh” and ultimately ruins the project. http://scratch.mit.edu/projects/10750409/

I can't seem to get the projects to save the list's properties correctly, so maybe the Scratch team could help debug these. The lists should stay in the layer they are in when the project is saved, and they shouldn't shift their position or change size.

Okay, nevermind about the second link, it just takes a manual save to fix it. Automatic saving seems to not keep the original position and size of the list.