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very strange. what exact version are you using?
are you sure you are not sitting on your Wacom or something? this could be a Wacom, mouse, keyboard issue, or some strange acting up of your OS. did you restart your software? if that did not work then restart the Computer. try to check your mouse, keyboard, wacom - I have had situations that a crumb of bread was stuck somewhere and I was thinking someone hijacked my PC.
if all else fails try to reset your preferences Ctrl+Alt+Shift+ launch Ae App and click o.k to reset preferences.
update on the results!
I don't think it is a mouse or keyboard issue because it doesn't have the same problem on any other "layer" based program. I did restart the program and the computer and it didn't work. I will try to reset preferences.
Resetting the preferences fixed the issue! Thanks so much!
Yes! we did it! probably a corruption of your pref file. there isn't any preference that says "click on a layer and make a mess" but there is a lot of text in the pref file and some strange occurrence can corrupt that file I imagine.