Ok so I've disabled the Skirmish in Base.rte and Missions.rte and I still get the vanilla actors. I disabled UniTec's and I can't really think of anything else to do.
The other activities in the other mods are activated.

Anybody have any other suggestions?

Disable mods one by one until you find the one (or more) that are insisting on you using the default actors, and then either don't use that mod, or find the activities file it is including and comment it out.

That's what I've been doing.

So I just figured out that the Astro mission has a bit of bug I think?

So the activities file that it has, when its activated, I can play Astro and the vanilla skirmish is on. When I comment it in the index, Astro doesn't show up on the Campaign screen but the vanilla activities is off.

It's not really a bug if you have to modify the mod to make it occur. It just so happens documentation wasn't included to tell the user not to use that Activities.ini.