The paint tool in the terrain editor won’t work correctly if “Auto Material” is toggled somewhere else (such as in the “Add” section).
From the looks of it, somewhere internally the paint tool is operating with the auto material settings. This means no matter what material you have selected, it will paint the same material onto the same existing terrain.
There is no way to disable auto material for the paint brush. You have to instead select the tab with it enabled (such as “Add”) and toggle it off.
This started happening about a week ago. It occurs in Roblox Studio version 0.413.1.370526.
This might be related to Selecting Paint tool after selecting Flatten tool causes Paint tool to not function, of which a fix is already pending, but on the off-chance it’s different, I thought I’d report it anyway.