Here's are a few updates from various members of the dev team:
Black Dyes: I'm sure you know that black dyes were tweaked on Halloween, and I'm hearing from players that they're really pleased with the look, now.
Dye Recipes: I'm told that any combination you attained with the earlier dyes should be attainable now. Yes, it's true there is no Dye Remover any longer, and obviously grey dye doesn't offer the same function. But you really should be able to find a new combination that attains the same appearance.
Stacking Issues: It turns out that nearly all items in Nightfall have a special "flag" on them, and that flag has been preventing the stacking of items. Now, I told Jeff this morning that this isn't a universal situation, because, for instance, my Tanned Hides and my Cloth are stacking just fine. (He responded that perhaps not all items have the flag, which would account for some items remaining properly stackable.) The issue has been discovered and a fix has been added to an upcoming Live Build. I believe you may see the update on this as early as today. We apologize for the inconvenience with this. What a relief to be able to tidily reorganize our vaults and bags, huh?

Special Dye: The "To Dye For" mission (which you obtain in Kamadan) gives you a special dye, one is spawned differently, and this dye will not stack now or in the future. However, you will get that single dye just the one time, so if you keep it, you'll have just that one unstackable square. (I used mine right away, to avoid using up a space.)
AI Issues: We're addressing AI issues in the here and now, as reported in this thread. I will probably have more to share on that later.
This is not an all-inclusive list, so please don't despair if there is something about which you're concerned that didn't make this informal list. The list is just a "fly-by update" on a few issues that we know are concerns, and I'll post more as I am able.
