Not sure what is happening.
Kart-Hadast had an income of 1301.
I destroyed* the 2nd lvl colony building and income dropped several hundred.
I process-cq rebuilt it, and income was over 2500.
Which seemed very strange.
So I reloaded the save and took the Governor out and did the same thing.
Income went up to over 1900.
Reloaded and just took the Governor in and out. Income again jumped up more than thousand from the 1301 base.
I then went through every governed settlement I own and pulled the governor in and out. Some settlements stayed same, some went up a few hundred or even a thousand or more, and Gader went up several thousand. None went down.
I have not noticed that with settlements before.
*I thought I might have a building 'hidden' below the 3rd line.