It is hard for me to read from your post what were exact circumstances for each kill and the result, so I can only guess. If I understand you, it seems, there are troubles to get a kill counted (or loot mission mats) in case you use enchants, right? I think that you will not get a kill counted if you only use enchants. Maybe a problem with the lock system?
Do you see any difference when you never/always use enchant? Start combat with enchant/spell? End combat with enchant/spell? Never use magic? Can you check if you have lock on the target in each case?
Do you see any difference when you never/always use enchant? Start combat with enchant/spell? End combat with enchant/spell? Never use magic? Can you check if you have lock on the target in each case?