Hello,
to clarify: It doesn't only happen after level six. For my engineer commander lvl 3 weapon does not show.
If I remember correctly it happens for this commander:
Morph 1:
Metal: 225
Slot 1 (Weapon): Lightning Rifle
Slot 2 (Module): CarRepairer's Nanolathe
Morph 2:
Metal: 650
Slot 3 (Module): CarRepairer's Nanolathe
Slot 4 (Module): Lazarus Device
Morph 3:
Metal: 900
Slot 5 (Flex Wep): Lightning Rifle
Slot 6 (Module): Flux Amplifier
Slot 7 (Module): Advanced Targeting System
For lvl 3 the Lightning rifle doesn't show. It says: much purchases: 2 in help for the lightning rifle so I thought I am allowed to equip two of them. I only tested in multiplayer. I will test again to verify but its hard to test in multiplayer because if I focus on my commander I'm dead before I reach lvl3. I would need a dummy player to test. Any volunteers?