seeing from your description, it could be many factors, I don't know the game you mention, but I played some of the RTS game, and sometimes the game like pausing.. once I think it was my graphic card, but after I upgrade it, it still there, and this game that I played is not 3D RTS.. sorry, I forgot the name, if it's not mistaken it's kingdom under fire.. perhaps you can look at your hard drive activity during the slowdown, if it's because the hard drive, you could upgrade the memory or upgrade your hard drive.. if it's not it could be the processor because of many objects that the processor handle
hope it helps..