I mined some Naquadah Ore from SGCraft with a Fortune 1000 Diamond Pickaxe (I have cheats enabled, and switched from creative to survival), but the gems from said ore sometimes do not stack IF they are placed into a Handy Bag from the inventory, but always do when inserted from the hotbar. Stacking is hit or miss within the handy bag as well until I move the gems into the hotbar and put them back. None of the gems have any NBT associated with them.

It might be SGCraft's fault as well, but since the items are identical (According to JEI and the Advanced Tooltips), I am leaning towards this mod being at fault.

Minecraft 1.10.2
Forge 12.18.2.2151
Ender Utilities 0.6.5
SGCraft 1.13.1

I just found that if I hover over the old, non full stack then move the gems to and from my inventory, it works. So this might be SGCraft's fault after all.

Paging @gcewing

Toying around with this some more, and it seems to be a desync issue. I can pick up a stack and place it on another, and the stack I am holding will go into the stack I clicked on BUT won't be removed from my hand. Closing and reopening the handy bag seems to resync it and causes the phantom stack to disappear.

Weird.

Yup. It's a desync issue. The same thing happens with redstone.

As I have over 200 mods, that might take a while.

I only started seeing it after updating to the Forge version I posted, and now I am seeing it in other inventories/GUIs as well (from Vanilla and other mods), so it may be a Forge issue. The previous Forge version I used didn't have this issue (I think), so I will try going back to it and see what happens.

Hmm, well at least for me in a minimalistic test instance, the Handy Bag inventory works perfectly normal with the latest Forge build 2179.

Wait, are you saying vanilla redstone also has desync issue in the Handy Bag? O_o

There was a similar stacking issue/glitch/ghost items on the client side with the Blood Magic teleposer foci (or whatever they are called) a while back. It was caused by Blood Magic accidentally creating an empty NBT compound tag to the items on the client side when they were hovered over and it tried to grab the tooltip. This then results in the client side Ender Utilities inventory code to think that the items can't stack with ones that don't have that empty tag, but the server side is what ultimately knows what is actually going on and decides what has actually happened, so re-opening the GUI re-syncs everything from the server to the client.

But if this happens with redstone... does it happen with EVERYTHING? Or do you know if some mod might be adding an ItemStack capability to certain items or something? Or maybe another mod has a similar bug with getting tooltips? Does anything add any special functionality or tooltips to redstone?

Edit: And as far as I'm aware, there shouldn't be any desync or stacking bugs in Ender Utilities related to this, I haven't seen any while testing stuff in my test worlds, and also some of the Youtubers I'm watching regularly use Handy Bags and I've never seen an issue like this.

There was/is however one bug in the current release version, where if you try to click on a slot that has a max stack size limit and an item in it, with more than one item in the cursor, it will delete all but one item from that cursor stack. This is mostly a concern if you try to swap out existing modules while holding more than one (which normally wouldn't be allowed at all, but due to the bug it did allow swapping it but it deleted the extra items...). It has been fixed in the repo since a looong time ago, but I haven't made a new release since the end of July... I'm hoping to get the next release out soon-ish though.

It is also possible that some other mod could be interfering with things. Is this a large modpack? Does this happen reliably all the time in your pack/world? Are you also able to reproduce this if you make a new instance and a test world where you have only Ender Utilities, SGCraft and JEI installed? If it doesn't happen there, then it is most likely some other mod interfering with my Container/GUI...

In that case, to find out the cause, you would have to do something like either start with an empty instance or a copy of your main modpack instance and start adding or taking out mods until you find the one with which the issue starts appearing. It's probably easier to start with an empty instance to avoid the complaints about missing mods each time. Then throw in a small amount of mods at a time until the issue starts appearing. Unfortunately that can be rather tedious work...

I am on 2179 now, and I am about to go out mining, so we will see what happens.

I still need to build the rest of my bunker as well. That's going to take several days, at least (real world days, not in game days).

I am no longer seeing this. I will chalk this issue up to a Forge bug and close it.