This problem is caused by EfficientSmelting, their mod messes with things it shouldn't, in this case changing the stack size of items flagged "not-stackable". You can report this on their page, it also seems that their mod has a "Stack size multiply" setting which you could disable to potentially fix this problem. However, I would personally recommend that you remove EfficientSmelting from your mod list as this same problem was reported on their page 5 months ago and the mod was last updated 2 years ago.