I'd follow default config with a menuconfig just to make sure what you need gets loaded up.. Worth a shot..
I have tried what I could think of without any improvement..
Edit: What I think is happening is
cpu scheduling going on a per user basis, 1/2 for user 1/2 for root available. As I can run the same thing as root and only get 50% but I can run one instance as root and one as user and get 98% load..