I'm using the updater but am having a problem with the exclude setting (I'm currently using a different tradeskill window).
I go into ignored, find the file and double click and the line turns red, I click okay and get the message 'please go to settings and check the files you want the updater to ignore' I go back into ignore and find the line I had checked to be reset.
And it does overwrite the file if I click update.
Settings file is not affected by any permission restrictions, so it's pretty likely that it is just corrupt. The "Please go to settings..." message will only show up once after installing the updater.