The attached level 6 character is missing two magus Arcanas.
What I did:
1) Created a level 3 Dwarf Magus. At this time there was 1 Arcana available. I left that blank since I'm playing a card caster (http://www.d20pfsrd.com/classes/base-classes/magus/archetypes/paizo---magus-archetypes/card-caster-magus-archetype) and PCgen does not yet support that type. I'm keeping track of that in notes.
2) Loaded the character and added 3 levels. A second Arcanas should be available now.
Starting at 3rd level, a magus gains one magus arcana. He gains an additional magus arcana for every three levels of magus attained after 3rd level.
3) Under Feats & Abilities -> Gained it shows 0 Magus Arcanas
The only extra twist I see here is that the character has a GM awarded +1 Feat.