If it works with your fel runebook, I don't think it is a script problem. Sometimes it matters where you mark your runes (such as if you are close enought to the trees and what not). I am a big fan of MWinc, both lumberjacking and mining, and sometimes I have issues of where I mark my runes.
I have not tried jacking in Ter Mur, but I would start there, maybe only mark one rune (with an empty book) and try that. See if you have to be is special spots or some weird nonsense.
Did you see if you can even chop there?