Are you using MC rounds for your weapons? A energy weapon with 20 base DAM will do 35 DAM with an MC round, which should be more than enough to surpass the armor of almost anything.
None of my energy weapons will switch to alternate ammo. The only weapons I've been able to go to alternate ammo with are the 9mm pistol and the Service rifle. No other weapon switches between ammo types. I'm guessing it's some sort of bug. Others have reported ammo switching issues so I saw no need to report it again.