The Make Square checkbox just ensures that the two size numbers are the same. If they are already the same then there is no change to apply. If they aren't then one of the numbers will change and the Apply button will be enabled. (The state of the Make Square checkbox itself is never saved. When you open Preferences, it is inferred to be set if the two numbers are the same, and cleared if they are not.)
Confirmed! Looks like that has been broken in Beta 4. We'll get that fixed.