Am I the dumb one?

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Ah. In this lies the issue.

I always add He first, and then the O2, and then blast in the air on top to get everything circulating nicely.

I've missed the mix, not enough for a rebreather to care, but never waited for a mix to settle out. I would mix 8 444 cu ft at a time.
I too would fill slowly, then at the end blast some air. There’s no way at the gases aren’t mixed after that.

I assumed the people having issues were filling slow and their measurements were distorted by the last gas in the manifold.

I believe the principle cause is temperature of the gases, don't quote me on that, I could be misremembering, a search here may bring it up, I think it has been discussed before.
But basically the different gases end up with different temperatures, He being lower than O2 and N2, which right after filling, bottle upright shows a lower He content than bottle upside down.
So, the homogeneous mixing happens when the different gas molecules reach same temperature(?)

Wookie, you're filling T-bottles. I've mentioned it seems the smaller the cylinder the more drastic the difference. Rebreather bottles being the best examples, and likely a 444 cf3 bottles being the opposite.
 
Bunch of interesting info here; I had not considered He, as I've only witnessed Nitrox divers doing this. Not surprised there.

It would only make sense that He would be affected by this, especially on a hot fill, based on the molecular weight (being the lightest gas on Earth behind Hydrogen)

H ~1g/mole
He 4g/mole
N 28g/mole
O 32g/mole
 
I would NEVER believe that rolling and rocking the tanks works, but I have seen it work too many times to argue otherwise - for PP mixing of nitrox.
 
https://www.shearwater.com/products/peregrine/

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