Quick update on this for you @OSRSteph:
I've had a look into this, and the issue is actually due to the presence of anchovies and shrimp in your inventory. It's actually a fun and really weird quirk of OSRS: if you have more than one cookable item in your inventory (e.g., shrimp and anchovies), the cooking interface will show cooked variants of those fish as options. If you only have one cookable item in your inventory, the cooking interface will show the raw version of the fish. Test this out yourself- it's interesting!
I've just pushed a script update: v3.20. In this update, the script will now search for both raw and cooked variants of the fish in the interface. This should solve all of the problems you were experiencing. The script already correctly banks items that you do not plan to cook, so this should not be a problem.
Good luck!
-Apa