Oblivion has a limit on the number of ground textures in a cell, and if more are used, then the extras are just ignored. I.e. another texture is used instead. Fixing the problem is a matter of determining which cell has the overflow, and then making sure the seam line uses the same texture in each cell. That sometimes requires changing the adjacent cell's texture as well.
Mods like QTP3 don't affect that, as they just replace each texture with a new one. The matching problem then exists between two new textures instead of two old ones, but it remains a mis-match. Only a mod that edits the cells will fix it.