tl:dr if too much math just give me a shot and do what i wrote in the end in bold and underlined, basically yea, just believe me
to help understand just why soot black is so hard to get having an understanding how it works in general may help, i'll try to explain to the best of my ability, if its to convuluted than sorry
Basically your chocobo color is determined by literal rgb values, the color that you end up with is the one roundet closest to the value that your chocobo is on.
baseline your chocobo starts at desert yellow, Red 219, green 180, blue 87. your values cannot exceed 255 and can not go below 0
when you now feed your chocobo than every fruit either raises 2 values while lowering a third +-5, or it lowers 2 values while raising the third +-5, thats also why feeding order is important, as the calculator will assume every fruit counts, so feeding 20 xelpathol apples say is -100 blue but as you would hit 0 blue after 17,5 apples (if starting from desert yellow baseline chocobo) the last 2,5 apples (or -13 blue) wouldn't be accounted for meaning when you are finally done you end up with 13 blue more than intendet.
there is some rng involved, but its not completly cleared up how that came to be, theorys range from some fruit not registering to rgb values not allways moving +-5 but actually moving +- 3-7, at either rate the reason why you (and many others) end up kobold brown or ink blue is the following
sooth black rgb:43,41,35 (+119 points from 0/0/0)
kobold brown: 48,33,27 (+108 points from 0/0/0)
ink blue : 26,31,39 (+96 points from 0/0/0)
meaning kobold brown and ink blue are technically more black than sooth black while Also (thats what makes it so much worse) sandwiching sooth black kinda inbetween as both have 2 lower and 1 higher value , a different one at that.
the problem this presents is that you don't know your exact values, your ink blue chocobo could be exactly 26,31,39, or it could be 0,41,35 which would put 2 of 3 values at exactly sooth black level but still make your chocobo ink blue as the red value of ink blue is so much lower than with sooth black that it would actually match your given rgb values (0,41,35) 3 points closer than it would match sooth black.
Now even the calculator only knows your color, not your exact values so if you now tell the calculator your chocobo is ink blue the calculator will work with the assumption your color value is 26,31,39 and tell you to feed your chocobo to get its color values closer to 43,41,35.
If however your real color value is say 30,20,30 which would also give you ink blue than by trying to change your values from 26,31,39->43,41,35 you actually would go from 30,20,30->47,30,26 which would than again put you closer to kobold brown than to sooth black
unless you want to do a shitton of math yourself at this point your 3 best bets are
1 just use the calculator again, stop feeding the chocobo the moment you get the color change message, don't care how many more food it says to use, repeat until you get sooth black, should work out after some trys 99% of the time unless you are at some really fucked rgb values where you do an exact color bounce between two colors down to the sub value.
2.try to tank its values completly, so get it down to 0/5/0 or 0/0/5, (just feed like 15 apples/pears/berries in a 1/1/1->1/1/1->1/1..... way if you are allready kobold brown or ink blue, and get the most ink blue chocobo in existance), from there work your way upwards 17 apples followed by 8 plums (no alternating), should do the trick (with a bit of luck, again rng...)
3. if both fail. reset its color and start anew, though i would really recommend variant 1, it should work out given a few more trys.