In the Advance Players guide the Oracle's known spells are fixed and are not modified by an ability modifier.
I have an Oracle of Life at level 6. Left is the spells known number by pcgen and right is from the Advance players guide (table 2-6)
10 lvl0 7 lvl0
8 lvl1 4 lvl1
5 lvl2 2 lvl2
3 lvl 3 1 lvl3
This is not adding the bonus spells given by mysteries. As far as I can tell the spells per day chart is correct, in the meantime I've just subtracted the spells and wrote down the chart
windows 7 x64
So this took me a moment but I'll just say that the reason for the spells was really dumb. The above option was clicked off but there is nothing wrong. and frankly I'm embarrassed to say what it was.
Is the PCGen HouseRule Preference "Add stat bonus to Spells Known (BONUSSPELLKNOWN) enabled?
Making a test oracle, I get the correct number of KNOWN for a 6th level Oracle:
7, 6, 4, 3
1st +2 Added for bonus Spells added by the program
2nd +2 Added for bonus Spells added by the program
3rd +2 Added for bonus Spells added by the program
Thus, as far as I can tell, not using any House Rules, the correct legal numbers are achieved.
I can't debug the issue without a character pcg. Those usually hold the answers about selections and give an easier answer of "This and that combined to reach the answer you have." Please review the program settings, and if this continues to be an issue, attach the pcg file here.