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I've noticed the same thing in PcGen 6.06 and the last two 6.08's.
I'm creating a 6th-level Oracle using the PFRPG Core Rulebook and Advanced Player's Guide sources and have encountered what I think is a bug in the way spells known are calculated. (But I wanted to check here before creating a JIRA ticket in case it's user error.)
When creating an Oracle, there are three sources of spells: normal "spells known", which increase as levels of Oracle are added; cure/inflict spells; and spells from the Oracle's Mystery. The latter two use the phrases "In addition to the spells gained by oracles as they gain levels" and "These spells are in addition to the number of spells given on Table 2–6", respectively. However, when using PCGen's spell selector, the cure/inflict spells and Mystery spells are counted against the spells known. For example, my level 6 Oracle (with the Waves Mystery) should be able to learn three third-level spells, plus Cure Serious Wounds and Water Breathing. Instead, the latter two spells are counted against my three and I'm only able to select a single additional third-level spell.
I have ensured that "Allow Use of Higher Spell Slots" is not (and never has been) enabled and began with my third-level spells (though I've since added others and seen the same problem with all spell levels), so I'm confident that isn't the issue. My character file is available at https://gist.github.com/benblank/9f2a82e2cbd4255b8ff93d90911b645b.