Unfortunately, I have not found a fix myself. I asked a question/posted a thread regarding the same thing but no one has responded yet, haha. No one wants to waste the extra video cards! I don't think I'm allowed to mention it, but I assume you know of the other streaming program (which requires a payment for a premium license). It has options which fix this issue, while allowing SLi to run in the background. However I am still more a fan of OBS than of that, so I'm staying tuned for further updates that may hopefully address this issue...
P.S: I said before that this only occurs with newer drivers + newer versions of OBS, so perhaps tinkering with different combinations may fix your case, but that's not the best for overall performance. Also, I read that it's because OBS requires power from your GPU, and having two GPU's causes only 50% of the power to be drawn from the card that your Source Engine games are running on - but I can not be sure ^^.
EDIT: I found a solution, in it's own sense. Since CS:GO and probably most other source engine games are more CPU intensive than GPU intensive, the extra video cards probably don't matter. But for other games, it does. Since you are running SLi, you need to create individual 3D Program Settings for your Source Games which you wish to stream, i.e CS:GO. Here's how:
> Right click your desktop,
> Click on "NVIDIA Control Panel",
> On the left panel, under "3D Settings" (click on the little [+] box if you have to), click on "Manage 3D Settings",
> Under "I would like to use these 3D Settings:" click on the tab that says "Program Settings",
> Under "1. Select a program to customize:", tick "Show only programs found on this computer" and then click on "Add",
> Look for "csgo" in the list, highlight it by left clicking on it and then click on "Add Selected Program",
> Then under "2. Specify the settings for this program:", scroll down until you find "SLI Rendering Mode" and change it to "Single-GPU".
> Click "Apply"
> ???
> Profit!
Note: Make sure you have SLi Enabled.
Notev2: If you can't find "csgo", make sure you run the game before hand then try search for it again.
Notev3: If you STILL can't find "csgo", make these changes while the game is running in the background.
Notev4: To get SLi working for any other game, just do the same under the "Global Settings" tab, but change the "SLi Rendering Mode" to "NVIDIA Recommended".