If you selected the tasks properly and set them to stop by certain levels and select the right staff for every task this should never happen.
Will check out the bolt switching itself.
Pm me on Discord so I can take a look at your setup:
Khaleesi#2542
EDIT:
There was indeed a issue when you ahve multiple bolts in your inventory
Staff switching is workig just fine, so might wanna check that in your save file if you selected the right staff ^^
Khal Magic updated to V1.06:
- Fixed switching bolts if you have more than the task requires
- Added all Dragon Bolts (Enchanting)
Will be live in a few hours!
Have fun! ^^