Starting with a Lvl 1 Sorcerer with 10 CHA you will have:
A sorcerer’s selection of spells is extremely limited.
A sorcerer begins play knowing four 0-level spells and
two 1st-level spells of her choice. At each new sorcerer
level, she gains one or more new spells, as indicated on
Table 3–15. (Unlike spells per day, the number of spells
a sorcerer knows is not affected by her Charisma score;
the numbers on Table 3–15 are fixed.)
10 CHA = 0: , 1: 
11 CHA = 0: , 1: 
12 CHA = 0: , 1: 
13 CHA = 0: , 1: 
14 CHA = 0: , 1: 
15 CHA = 0: , 1: 
16 CHA = 0: , 1: 
17 CHA = 0: , 1: 
18 CHA = 0: , 1: 
19 CHA = 0: , 1: 
20 CHA = 0: , 1: 
Level Progression looks right in the cr_classes.lst to the best of my knowledge of how things work.
I can confirm that the check box for 'Add stat bonus to Spells Known (BONUSSPELLKNOWN)' is NOT checked (as noted, that in the Pathfinder Game System this should default to Bonus Spells being Off.)
Pathfinder Game System:
v6.03.05 (latest from Unstable Releases)
Load Core Supplements
Create New Character.
Human, 10's for all stats, level 1 Sorcerer:
10 CHA = 0: (4), 1: (0) - This is CORRECT as need a Charisma score of 10 + Spell Level.
20 CHA = 0: (4), 1: (4) - This is INCORRECT and should be two level 1 spells.
Turned ON BONUSSPELLKNOWN:
20 CHA = 0: (4), 1: (4) - Still INCORRECT.
Turned OFF BONUSSPELLKNOWN
20 CHA = 0: (4), 1: (2) - CORRECT.
The act of Force toggling it ON and OFF resolved the issue. Perhaps I turned it ON in a previous version of the installation on my computer at home, and the check box though appearing not checked, clearly had some residual effect. (though that doesn't explain my computer at work who had never had a version of PCGen on it).
Sorry to have wasted some of your time... I know you are quite busy with school.
if you can squeeze a look at this. It sounds like the preference setting is not absolute in all cases. All my testing garnered the correct results. But if you can see if there is something in the code that might not be quite so solid that'd be great. Thanks,
I'm also unable to reproduce the issue. I cannot see a way in which the box could be unchecked but the rule is still applying.
Thanks, James, for taking a look at this as well. At this time, I'm completely okay with this being Closed out – as this issue appears to be environmental and isolated to my installation/computer/instance of PCGen.
If you can come up with a reproducible case, please re-open. – david