I have been working with After Effects for a while now and I just ran into this problem today. I am working in After Effects CS6 version 188.8.131.52. I have used this for 1 month now at my job. Today I opened a project up and when I clicked on a layer it changed positions. It went from layer 1 to layer 5. Every time I click a layer it does the same thing. It just started doing this today and I have opened other projects and it does the same thing to them. I even created a new project and it did it again. After all of that didn't work I decided to uninstall after effects from my computer and then downloaded it again, and it still did it. I don't know what I did to mess it up, but I can't figure it out. If needed I can provide a video.
Check your system's graphics driver, screen and input device settings. Typically this happens when you use high resolutions in combination with DPI settings for the system and your mouse pointer is out of registration - in CS6's thinking, that is, since it doesn't support High-DPI screens. Similar stuff applies to tablet drivers and so on.