Ok, went back in and did some quick testing with the problem I had. Disabled the old Ramps and Roads pack so I wouldn't get confused on if I was using the old ones, so strictly using basic ModTerrain here.
First, created a simple baseplates, with a few pieces of modterrain bricks sitting on them. Without closing to menu, I cleared bricks and loaded save. All was well.
After closing to menu, I booted back up to bedroom and loaded the save again. For some, unexplicable reason, the x16 cube I had used for the demonstration didn't load (I was using x16s for the terrain in progress that didn't load before, so this didn't surprise.)
Odd part is, console isn't showing a error upon loading the save, and is acting like the brick just didn't exist in it (brick count of the loaded save said 6, where if I was counting the x16 I was using, it would have been 7.)
Unsure what's up o_o