When you click into /go over a hole made by hole creating tool or if you click into/go over gap in terrain (they tend to appear on chunk boarders), cursor of your mouse suddenly "jumps" under the terrain and far behind your current target. That leads to rather unpleasant results, especially when you are using flattening tool, because noggt will then try to flatten some area behind for instance mountain you are currently editing and it is trying to flatten it with spot deep under the terrain. That leads to creating huge and deep hole.So, how to avoid that? The best is to create holes when you are already done with terrain modelling in place when you want to have them. Otherwise be very, very careful around them. Never pass middle of your cursor over them while editing. If you use SDL 1.4, you should have Fix gaps function in Assisst menu. Use that from time to time to fix gaps between chunks of terrain. But it doesn't matter if you use this version of noggit or not - be careful around chunk boarders too and always watch for those damned gaps and holes in terrain.Thats all we can do about that, at least for now.
Fuh, have you tryed hole tool? Stupid question of me maybe, but if you did, I don't know what else could be done... I never saw anything like that to just simply appear.
You may try to upload your MPQ archive with your ADTs so we can just check them out peronally. Like I said, you've got me quite puzzled for now.