I would assume you need to select the 3D performance setting. This should disable your second card's output, but will allow both of your monitors to work (as they are both plugged into your prime card). The 3D setting should enable SLI for gaming etc, but because your GPU has two outputs they should both work.
Hmm this is a odd problem indeed. I got two monitors on my 9800gt sli setup. I am using older drivers though but I am with out issue. The only thing that I don't like is my ancient dell crt that limits my resolution. Try older drivers to rule out any possible driver bug. By the way what model is you 9500gt s?
I know this is 2 months old but I was having the same problem. After you enable SLI and it only shows on monitor enabled on your primary card, go to Display>Set up multiple displays. Then select clone, horizontal span, or vertical span. Thats what I ended up doing. Good luck.