I had hoped for the new version to have this fixed.
But I'm still getting the stuttering when new units arrive in the battlefield.

There's got to be a way for the programmers to fix this.
Preload/precalculate the content or spread out the work
over a longer time so it doesn't result in a CPU/bus/hdd/whatever load spike.
Use asynchronous I/O, a faster memory management scheme... I don't know... anything that helps.
I'd love to hear one of the developers explain what happens when new enemies arrive
and what seems to be the cause of the stuttering.
