Mood, and hence likelyhood of attack, is an individual factor for each village. This means that one village might be pissed off and send its warriors to attack you, whilst another will grant you gifts. When a raiding party from one village performs an attack, the alarm level of the village decreases. In addition, the threshold for granting gifts is rather low: even with three green or cyan !!!s, natives from these villages might still grant you gifts.
Taking this into account, it's not so difficult to understand: You found colonies -> natives grant gifts, you improve the land and found more colonies -> natives become alarmed and attack -> alarm level decreases and natives grant gifts. Alarm level increases steadily as a result of your presense, though, and more military units means more alarm (even though keeping them in colonies helps). Thus, we have a cyclic situation.