The way I see it, the things that could be at fault are:
- The PC hardware (cables, PC)
- The software (drivers, antivirus, FAF)
- The ISP
- Your network
First, have you tried the d3d_WindowsCursor command in console? In game press ' then type the command. It should show an auto completed version. The slowdown in the game will look similar to lag/dropped packets. Check that after changing the setting it is the same.
Have you tried updating your drivers? Windows Update has a semi hidden section at the bottom for updating drivers. I had an issue with my USB controller. Every 45 minutes, it would cause the game to crash. Since updating the drivers to the newest version, it has been fine. I didnt know the section existed on Windows Update.
Although hard to do, have you tried your machine on a different connection to the ISP? For example, if its a laptop, try taking it to a friends house. Have you got a spare laptop you could try and run the game on, at your house? At least then you can rule out the ISP, Router and cables? I had a plastic connection on my old router that had degraded with time and gave me a poor connection.
Are you running antivirus/Firewall at the same time? I've seen antivirus stop things from working and also slow things down by inspecting the packets coming to your machine. Ive also seen firewalls break things. Try turning off the firewall while your play. If that fixes it, add FAF/Supreme commander to the antivirus/firewall exceptions.
Do you get the slowdown from the very beginning of the game or after a specific length of time?
I would go through the list and change things, one by one to see what is at fault. If you can narrow it down to one area it will help. If you can narrow it down to a smaller area we can go from there.