For the past month I have not be able to run the bot as there are no missions available to me. Did I miss something or is there a "setting" that is now messed up?

To reset your settings open menu->tools->open data folder button. Open it and delete. Restart bot. Login to your char manually and clear missions in journal. Default courier settings are working one. You may change agent level to run depending on your faction standing to caldary state. Faction standing 1 opens 2 lvl agents, faction level 3 opens 3 level agents and if you have faction standing 5 and omega clone you can run 4 lvl missions. Standings are checked in character sheet.

When you complete your settings setup, redo first run. Don't switch algorithm from courier to something else, and make sure you are in industrial ship before first run.

If you edit default settings make sure you have at least 10 available agents of selected level in high sec connected to your home station. You cannot travel through low sec systems to reach agents. The less agents you have the more frequently bot have to stop to not loose standing. If you don't care about standing disable "never drop standing" option. Bot may revisit agents where missions were declined within 4h.

If nothing will help contact me.