From vanilla, so far I've only seen item frames, which is what made me realize this is an Iron Chests issue and not a FoodPlus issue. From FoodPlus, Rice, Tomato seeds, and Cherry tomatoes don't show up. I've not had any problems from other mods, but I also don't have much experience yet with crystal chests. The space that the item WOULD be taking up is consumed by emptiness - for example, if I put item frames and sticks in the same crystal chest, the sticks are visible, but they're smaller and in a corner.

Deleted previous comment; was inaccurate. It seems to be caused by how MUCH of an item there is in a chest. Having two full stacks or more triggers the disappearance, but 127 is fine, suggesting that a byte value is being used to count the total of an item where a full size int or at least a short should probably go.

I'm going to close this issue and make a new issue that doesn't have information I've discovered to be inaccurate.