I'm now midway through cycle 21 and seeing what appears to be a huge mother load of emerald in Pharynx (the gauge is 2/3 full). However, once I actually go in there, there's none to be found.

This isn't the well-known AA bug, this is long after the mine quest and I've mined dozens of veins already. Out of desperation, I even turned on the physics mode through the console and went to every spot that could be a deposit, and the only one that's not already "spent" doesn't appear to be active yet (I tried drawing the glyphs over it anyway in case it just wasn't flashing, but nothing happened).

Could this be a bug? Could it be because most of the mine has already been mined, that the game choked while trying to choose where to put the color? Or is there some super-secret area in here (other than the easter egg) that I haven't found? It's driving me nuts. The game also reported a large azure deposit in this cycle and I was able to find three - yes, three locations for it in the same mine. But not a single emerald, anywhere.

Or, possibly the color is from something other than a vein? But if so, then what? I've been running around for an hour and haven't seen any of the bubbles, and I tried using Bait on both ends and nothing came. And there were a few "plants", but I already picked all those up and it still says there's a ton left when I exit the mine.

Does this ever happen? Does the game ever report color somewhere where it doesn't actually exist or you can't get it? Is that why this phase is called "confusion?"

I think, floating blobs and the little critters count for that display.

Not sure the hostile creatures count though, not sure.

As far as I can tell, the only things "alive" in there are a bunch of jumpers, and they don't give any color when killed. The critters would definitely come when Baited, and the floating blobs... well, the amount of color shown in the tool tip implies that there'd have to be at least 2 or 3 of those and I don't see a single one.

Anything else I could be missing? Is there perhaps some way to get up to those upper walkways that I'll only find out about later in the game? I know that veins are notoriously hard to find in this game, but I'm almost positive that they simply aren't there in this case.

Make sure you check for veins on the ground. They can be hard to see, especially on this map.

And the blobs of Color sometimes disappear for a long time before reappearing. I had a similiar situation where I couldn't find the 'missing' Color that was displayed on the map. It turned out there were a couple of Color blobs that only seemed to show up if I hung around long enough.