So, since you said you don't like the dark look of the fuel at the bottom, I'm guessing it is a translucent plastic tank, like an IBC?
I'd try to take some samples from near the bottom and from at the bottom. Put those into clear jars so you can better assess what's going on. Like you said it could be a different ratio of your stabilizer, especially if you are overdosing it, or at the bottom there could be sediment or
water.
You could also try "magnet fishing" in the tank to see if the darkness is rust, a magnet would get fuzzy with rust particles if they were present.
I've had success with "cleaning" tiny amounts from outdoor power equipment and jerry cans that have gotten water or dirt in them. Drain into a clear container, let it sit. Often the dirt gets caught up in the water, so when I decant the fuel I just leave the blob of water behind. I had a can of diesel with a half-pint of fuel, a half-pint of water, and some debris, I swished it out of the can into a jar where it was a milky mess. Wait a week, and the fuel is perfectly clear with a blob of dirty water in the corner of the jar.