EDIT:
Still an issue as of 2/7/18
EDIT:
Still an issue as of 3/2/18
EDIT:
Still an issue as of 3/9/19 (1.2.11)

I've recently been working on creating a command block based map that uses a trading system. After creating a command block system that would function as a trading center, I tested the system to find that 2/3 command blocks work as normal.
The first command block is an Impulse Non-Conditional that is powered by a button, which would clear a certain amount of a specific item from the nearest player's inventory, which then leads onto the next two blocks.
The second command block is the one that is broken. It is a Chain Conditional command block, which activates once the CB behind triggers, and is supposed to give the nearest player a certain amount of a specific item. Now, the problem isn't the function, it's the execution. I would press the button, and then the first CB would work as expected, and then the third block, which also a Chain Conditional that sends a title command to the action bar indicating a successful trade, would send out its message, but no items are given to my inventory; that is until I press the button again, to which then it takes more of the trade item out of my inventory, and then gives me the item, but only the yeild from the first activation appears until I click on the icon and the correct amount appears.

For Example:

32 Rotten Flesh for 2 Golden Apples
1.) Presses Button, 32 Rotten Flesh are taken from my inventory
2.) Actionbar message "You have successfully traded." appears, but the Golden Apples are not in my inventory.
3.) I press the button again, which takes 32 Rotten Flesh from my Inventory
4.) I receive the original 2 apples.
5.) I open my inventory and click on the 2 apples, and then it updates and the correct amount of four are now given.
6.) Actionbar message does not appear.

This pattern repeats forever.

I can confirm that this isn't of my own error, as I have footage of this command block system working as intended from the person I got the design from (see video here:https://www.youtube.com/watch?v=rNcVBbyjkpc)
At some point between that video and the present, this bug came to be, I don't know when, and I don't know why.
This bug is important and ruins intended game function, and thus should not be passed over.
I have been treated horribly before by the Bug Tracker people, as they have simply brushed me to the side and never addressed me again after hearing my initial case. So please, hear what I have to say before discarding my post, this issue, and me.