You can find this tool at:
Tools->Fix Tools->Effect Square Fix
which spawns a msgbox that says:
Forcibly fill the green effect square of all combos in the quest?
What is this green effect square?
What is the green effect square?
Green effect squares is the Devil!
Normally, the green square is the start or continue point of dmap, whereas the blue squares are warp points.
(I have no idea who wrote that, and I'm also not going to bother trying to find out.)
According to doAllEffectSquare() and doBlankEffectSquare() in zquest.cpp, this seems to be what it means to "fill a green effect square":
combobuf[i].walk |= 0xF0; //Effect
Still pretty cryptic, if you ask me.
Ok, so you mean the arrival square? Why is it bad?