Self made textures vs included

[CX1]

I am not sure if I should post here or on Editing forum, since it is only slighty connected with DoomBuilder (but it is).

Anyway:
DoomBuilder allows importing external texture wads. But I also made my own texture in the wad I am editing. That caused quite a mess among patches used for building the textures - they are assigned incorrectly.
I didn't use any name twice. I didn't even create new patch - just used existing ones to create new texture. So what may be a reason for that problem?

[Shadow Dweller]

do you have XWE?

EDIT: also check under doom editing, "custom textures". i had a similar problem. hopefully it will explain some things.