Here's my understanding of auto-tax and its effects:
In VI auto-tax adjust for a minium of 120% loyalty. You only get rebellions if loyalty is under 100% . HOWEVER, events that happen after you hit End Year may affect loyalty and the Auto-tax is not adjusted till your turn comes back. These events most commonly are :
- your king dies and new one with less happiness bonuses takes the throne
- your king is cutoff because enemy blocks a sea lane or he moves to province without a port
- province has a famine or something similar (although I think this takes a whole new turn to take effect)

Now there is some confustion on the 120% loyalty and faction resurrection. From the numerology thread on www.totalwar.com I understand that faction reemergences can spread to provinces with loyalty above 100% and less than 120% . However, for a reemergence to start , a province with less than 100% loyalty has to exist . If this province used to belong to the dead faction, a rebellion that starts there can transform into reemergence. Once a reemergence is occurring, other provinces can join it if their loyalty is under 120%. So the following (theoretical) scenario can happen:
You are Spain and you have wiped out Egyptians and are sitting nice in Palestine, Sinai and Egypt. Egypt has loyalty of 130%, Palestine 115% and Sinai 110%. They are therefore ALL GREEN when you hit the end year. Now, Turkey has Arabia (old Egyptian province) and their loyalty there is 80%. An Egyptian reemergence rebellion starts in Arabia because it is under 100%. Now Sinai and Palestine can JOIN the rebellion because they are under 120% [message comes out: long lost heir to Egypt leading reemergence in Arabia. 2 other provinces a joining in the rebellion or something like that]. Egypt stays loyal because it is over 120%. Result: you have a rebellion in provinces with >100% loyalty.

This is why auto-tax aims for 120% loyalty.

I hope this clarifies things.

afrit