I'm also on the side that finds this very distracting and not at all helpful. I agree that a different, more obvious change would be better than the subtle change happening now. If the colour can't be changed, since its part of the UI coding, then I would prefer not to have it at all.
Okay...I just went to confirm some of what I was saying, and its all changed again. I'm not quite sure what to make of it now - I need to use it a little first to see how functional it is (or isn't) :)
What I really want is the CSS code so I can make it function in whatever way it works best for me!
This happens because of the 'flickering' or highlighting or whatever you want to call it when you mouse over that row. The mouse location is the variable that changes the row colour and makes the darker, multiple item rows turn lighter. This is also changed with the latest setup.
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The last three column widths are still too narrow. The "Item Name", "Move to Shop", "Move to Vault", "Move to Wardrobe", and "Move to Armory" columns widths should be decreased just a bit
Also, to solve Iridescent's issue, maybe the first two rows could be fixed so that when you scroll down the page, the first two rolls scroll down along with you and therefore it'll be easy to see the names?
I understand that. But thats not what i am saying. :) Perhaps its is due to my layout choice ? im on morostide.
Currently, there are 3 row colors. dark orange (i assume this color changes based on layout), white, and the faded-blue-ish-white.
At the moment Any row you mouse-over currently turns into the faded blueish white color. In the screenshot I am moused over Cave Jelly (4). It was orange prior to that.

My question was, it seem that dark orange colored row was meant for items that had more than 1 in terms of quantity. But in QS thats not the case. ATM, both the faded-blue/white color and the orange colored rows are used to indicate items with multiples.
TLDR, This might be too confusing for me to explain in words.
Oh, I see, I misunderstood your issue. I thought all stacked items were dark orange unless you mouse over it. I can see from your image, that's not the case. I'm pretty sure it used to be that all stacks were dark orange (or whatever colour based on your layout). I hadn't realized that changed :(
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What bothers me more is the width of the columns. Item Name should definitely be wider and the move to ones should be smaller. For that reason, I miss the old QS page. ;O; (same can be said of the battle page where the opponent and your battle pet should be 50 / 50, instead it's like 75 your pet / 25 opponent squished in the corner yuck)
I hate this new quickstock. Maybe its because I'm using a large widescreen monitor, but "Move to Shop/Move to Vault/Move to Wardrobe/Move to Armory" are super long and stretch the page. The other columns are thin. Perhaps make it so there is a max column size? Or just make the "Item Name" column adjustable and the rest have a set size?
Also, the highlighting thing is just buggy. The column headers and where it says "stock" should not be able to be highlighted.
Also, I noticed that sometimes stacks are highlighted with color (as they should be) and other times they're not. There is no consistency.