I went through the autoexec that this tool creates and tested each variable and found that when running SLI you MUST delete sys_spec_postprocessing=3 from the autoexec.cfg file. This causes MASSIVE black hole flickering due to all SLI profiles using a custom postprocessing setting. - sys_spec_postprocessing=3 [custom]
I hope this helps another person that wants to use this nice application when running SLI.
Here is a link to the app if you have not tried it yet.
http://www.gamesas.com/forums/viewtopic.php?f=40&t=12953&hilit=application+1.5