Earlier this year, I had the same issue between two dropper bottles, bought several years apart.
Vallejo Game Colour Filthy Brown used to be the perfect base for my skintones. But since most of my miniatures have just exposed hands and faces (if even that), one dropper bottle went a long, long way. But mine finally showed signs of becoming empty, so eventually I bought a new one.
But to my dismay, the paint in the new bottle was way, way off in colour! The old one was much less saturated, and a lot less yellow.
I posted about it here on the LAF, and I eventually contacted Vallejo customer service. They were really accommodating, but could not help me further.
They could tell me that a couple of years ago, they did a recipe change for their entire VGC range, and the difference stems from that. They offered to send me a replacement bottle, but that would be the new formula too, so would not help me one bit. Also; I wasn't in it for a free bottle of paint, and I respectfully declined.
But this might be the very issue you encountered here too; there may be a difference in tone due to your two paints being made with differing recipes...