Technical Difficulties
I think limiting the maximum number items that can be refined through this option can be a quick fix. It was not designed to refine 96 items at once from 0 to +4 and after a lot of clicking, maybe something is being lost. I'm glad it was an item with low value. I would suggest refining them 10 at a time and you should have no problem.. the npc has worked for everyone for many years, I'm not sure we should try to troubleshoot the logic for such extreme and rare scenarios.
If you use a macro to auto click the refine, maybe lower the speed of the click, or do it manually and see if that fixes your issue.
If you use a macro to auto click the refine, maybe lower the speed of the click, or do it manually and see if that fixes your issue.