Ahh that explains the reactivation problem too. I sandboxed this version of TaskPaper, which means all preferences and files like that are stored in a new location. Use Window > StyleSheet > Open StyleSheet Folder to open the new sandboxed location. The old location (for Paddle version of TaskPaper anyway) is:
/Users/<username>/Library/Application\ Support/TaskPaper
I guess next thing is for me to rediscover why I didn’t sandbox it before. :\