Definition 1 is negative. I'm guessing so is Definition 2, because of 'stubborn' and 'regardless of the consequences'.
1. I'm flummoxed: Why? Doesn't the noun will connote positivity (its etymology: http://www.etymonline.com/index.php?term=will&allowed_in_frame=0)?
wilful = ...c.1200, "strong-willed," usually in a bad sense,...
2. What's the term for this phenomenon, where the noun is positive but the adjective is negative, and vice versa?
3. Are there other words subject to this paradox?