Before I describe what little more about it I know, let me clear two things up. I will be referring to a "virus", but I don't know what it actually is. I may sometimes say Gundam instead of mech. That's because I just spent 30 minutes looking up Gundam, not because it's a Gundam anime (although it might be).
So, I know it's a mech anime. When they enter the mech, they pass through a circle that applies a form fitting suit that they use to control the mecha. (I'm actually not totally sure about this).
One of the episodes involved a conference and/or other group of people collected together talking about the "virus". One of the attendees is infected (and there's something about them they have to hide to prevent people from finding this out).
The "virus" bas stages (I think) eventually takes over the infected (while they are in a mecha), and the infected loses control (becomes controlled?). If I recall correctly, the inside of the mecha now looks like a fleshy hell pit created by the "virus".
I'm fairly certain it was on Toonami. I'm 100% certain it was on T.V. in the US sometime between 1998 and 2005.