How are you calculating the profit per second? Because there are two very important factors here:
-What ship speed are you using
-What cargo quantity are you using
Because when FL Companion is at default settings it works out profit per second based on an average cruise speed of 280 m/s when in actual fact most transport ships have a cruise speed of 350 m/s.
With this issue appearing I recommend removing profit per second and changing it to profit per unit.
If we take your first example, neon to Kyushu I believe you are using a single unit to work out profit per second - that's good, However your profit per second is different to mine. My calculations are giving me a profit per second of $255 not your $219.