If I use sculpt or smooth , straight over terrain ( directly top down as you suggested) or even paint mode, then ya it still does it.
I almost feel like apologizing, given I seem to have my share issues with terrain editing, but at least I fixed it with smooth tool < can’t use detail smooth >, but now this.
If I’m to upgrade to 4.6 and I’m certainly willing to, I must know if stuff like this has been fixed, or if its not that, I kinda need to know why its happening 
Cheers
nl