Since 10.4.0 Mail has had this problem.
Go to Mail/Preferences/Rules enter 25 or more rules and the rules entry window will overflow off the bottom of the screen, taking with it the control buttons.
Apple phone techs, Apple Store geniuses, Apple Engineering have repeatedly confirmed this problem over the last 5 years. Apple Engineering has repeatedly said they are working on the problem. I am guessing its no more than 4 lines of code.