Not sure why they wouldn't reset, I tested this spot heavily. I can extend the refresh route as that seems to be the problem! For now, perhaps try a different spot?
Apa
No; follow the instructions in the pop-up message! You need to head to lumbridge and talk to the ranged tutor. This allows you to auto-equip arrows when you pick them up, instead of going via the inventory. You will need to set this up for ammo looting to work.
Not sure what you mean; it shouldn't log out unless you run out of resources. I'm not sure why it would stop otherwise, unless it wants to world-hop.
Are you sure you didn't externally stop the script?