So, after much testing I seem to have isolated my lag problem to this.

Consistently after 25 seconds (give or take), even without any input in the setup stage of a skirmish my framerate and timescale drops from 150-200 fps and 1.00x to 40-50fps and 0.40-60x respectively.

This drop in performance does not recover, and I only get the high performance in the first mission/skirmish I begin on starting the game.

During the time before the drop the game can clearly maintain the performance as multiple crafts/bombs/actors can be spammed smoothly with no lasting effects. However, after the drop the game performs even worse during explosions and particles onscreen.

Any ideas would be appreciated, but I have tried: 1 + 2 keys, Ctrl - O, reinstalling, settings.ini fiddling (deltatime ect) and reverting to vanilla.

What's your resolution? The second one sounds like what I get, and I have it fullscreen at 1280x1024.

Record some system statistics over time, I'd love to see if the lag begins with any large ram use or something.
Oh, and Mac/Pc and Intel/AMD?
Also system stats would be appreciated.

Thanks for the replies, I've got a PC running Windows 7, Intel Dual Core 2.13ghz and 4G of RAM. I use the basic 640x480 VGA resolution in fullscreen.

I ran task manager during play and my memory usage remained constant, and CPU usage fluctuated around 50-60%, there was no noticeable change when the lag started. My CPU usage did spike occasionally to around 85%, but this doesn't effect the game before the lag. Is there any other info I can get? I'm not really sure what you need.

Well, Windows 7 is out of my league, but that's exactly what I asked from you.
Huh.
Does anyone with better Windows familiarity have any idea what could cause this?
I am sorta expecting it to be a "strange inexplicable phenomena" though.

Are you running the computer brain mod, 'cause that's a real killer.

If not it might just go over in about 1-3 minutes.

Hey, I just thought of something.
Does your machine have adequate cooling?
I have noticed that CPU throttling occurs when the heat begins to go above 60º C on my computers, unless the fans can pick up and deal with the extra.
That could be why you get some great speed initially, and when the heat increases to the throttling minimum point you suddenly loose performance.

I had to help vacuum out a friend's PC yesterday, he assumed that dust was not going to get into it if the fans were on. ><;
After that the fans performed much, much better. The heatsink was more grey powder than it was metal!

That's an interesting idea, I'll get some CPU temperature measuring software and check it out while running CC. Thanks!