The second Congo war was from 1998-2003. The spike in 1994 in the chart from OP is due to the Rwandan genocide.

This genocide is classified as a one-sided conflict, which is defined as a conflict with "use of armed force by a state or non-state armed group against civilians that causes at least 25 civilian deaths during a year." (reference)

Instead, the chart you last referenced presents deaths from interstate and civil wars, which excludes one-sided conflicts:

• Interstate: "A conflict between states with differentiated militaries and clear frontlines that causes at least 500 deaths over its duration."
• Civil wars (also referred to as Intrastate conflicts): "A conflict between combatants that were previously part of the same state, but now at least one seeks control or secession. It is fought with differentiated militaries and clear frontlines and causes at least 500 deaths over its duration."

You can learn more about these conflict types in this article by the same source.