I just paid 1.1m to get me on a better standing with Farmers Alliance. It did work FA rep increased while Synth Food fell. So far so good. I undocked from the station, and my rep was set back to what it was before. Annoyingly the Synth Food is now permanently lowered and the 1.1m gone. Was it reset due to the faction I belong to ? If so I find it odd that I'm getting this bribe offered to begin with. I'm spending money on something and I'm worse off after ...
Faction IDs are "rep-fixed", meaning you can't go higher than to a certain point. The moment you undock, the reputation will get adjusted to the point where it is fixed. Similar to that, if you are using a Farmers Alliance ID on your ship and somehow manage to eff up your reputation with Farmers Alliance, once you dock, you will be full green with your faction again.
All IDs have something called rephacks which in principle ensures you for example cannot dock on a Corsair base as an Outcast, because that wouldn't make much sense.