Disabling that module did not help, I even tried with only this mod enabled but no luck. I did remember that I was able to harvest in the first dungeon that I cleared when I had no tools, so I sold all my fishing tools and I was able to assign some to the fishing job.
Viewing post in Mod: Automatic Tool Equip (ATE)
Alright. Then my best guess is that the ranking process for tools is encountering an error and aborting, which cancels the job assignment process. Are you using a campaign file imported from an earlier version of the game?
Also, if you could share your game log it would be really helpful. Any errors encountered should be reflected in the log, which helps me narrow down the issue.