Yeah, I would either let the charger do what it needs to do to equalize those cells, or individually charge the low cells like simplechamp said.
You can make a quick adapter by taking a really high resistor (like 100k ohms or more), and insert the leads into the balance tap for the cell in question. Then, clamp alligator clips to those resistor leads and charge that one cell. I like using the resistor because it helps keep the leads from touching by accident. The high value is needed so you aren't discharging while charging (100k ohms on 3.8v is only 38uA).
By the way, I like your "Lords of Death" avatar. One of my favorite movies of all time.
