I have not very long experience with dirt tanks, just a few months, but i have been running fresh and saltwater tanks with no dirt for a long time
My experience with dirt does seem to be somewhat similar to yours:
I started my first dirt tank with soil without any fertilizers, this soil was very black in color and had a high amount of organic labeled on the bag, it looked like a perfect soil to use. But this soon showed to be wrong, this soil colored my water very mutch. I used 2-3mm gravel as cap just as recommended in the Walstad book and elswhere on the internet. I did 90% waterchanges over several weeks, 3-4 waterchanges every week. At last i gave up and tried another soil, this soil was just the opposit, it contained what was not recommended: 30% cow dung
. This soil was lighter in color and did not color the water the same way as the first soil, after a couple of months the water get a yellow tint, but it is not combareble to the first soil. I also did change another factor in my substrate when using this cow dung soil that also maybe could have an effect on color/soil leaking to the water column, i change the cap to fine sand.
Dont know if this help, but i hope you sort it out.