I think I must just be really confused about how to use this tool and am missing something obvious, although I was able to use earlier versions with no problem. I have the exact same problem when I tried to follow along with your Map Modding guide (which is awesome by the way!).
https://www.dropbox.com/s/slqu1a50q3u1742/Ireland_chapter2.rar?dl=0 This is your example mod from the end of chapter 2 with the history, localization and common folders deleted. When I run mapfiller.bat it creates landed_titles.txt, localization, history/provinces and history/technology all seemingly fine. However it does not create a history/titles folder. At first I thought it was because of the addition of climate types to provinceDef.xls but adding a climate column doesn't help. What am I getting wrong here?
You have no holdings entered, could that be your problem?