Having the same problem on my server. I'm no expert at IC2 but I'm fairly certain that a Nano Sword can't take out a fully charged Nano Suit. And the losing charge on death bug is extremely annoying. Has anyone tried disabling Convenient Inventory or Inventory Tweaks? The losing the charge may have something to do with that.
EDIT: Tested in single player on NORMAL difficulty. Newly crafted Dark Matter armor = 1.5 hearts damage per zombie hit. Red Matter armor gets 1 to 1.5 hearts damage. Bronze armor is 0.5 to 1 heart of damage per zombie but it loses durability really fast. Gold armor gets 1 heart. Chainmail gets 1 to 1.5 damage. Iron gets 0.5 to 1 damage. Diamond armor does 0 to 0.5 hearts. Quantum and Nano (Fully Charged) Take no damage. Zombie does 2 hearts of damage WITHOUT armor. And in SSP there is no loss of charge upon death. I tested a Klein Star, a drill, an electric wrench, and the Quantum and Nano suits. I am 99% sure that both of these are server issues. Not client.