Open the log file in your editor and try to see what format the file is, perhaps it is Unix or Mac not DOS/Windows (Ansi) - try changing the format if you see it is not dos/win - Notepad++ makes it real easy, don't know about SublimeText. I can't think of a reason why it would insert the line numbers. You could try and edit TF.ahk and look for these lines (823 or so)
Else If (ReturnText = 2) Lines .= A_Index ": " A_LoopField "`n" ; add line number
and remove A_Index ": " part - that way it can never insert the line numbers - if the linenumbers are still there after this change they come from somewhere else.