I have a Steam Link and ran into this problem last night. I came here looking for a solution. After a little messing around, here's what I did to get it working.
* The Steam Link recognized both of my controllers, but FS only saw one.
* In the in-game controller setup, holding two buttons only worked for the first controller (the only one that FS already recognized).
* I was using wired X-Box 360 controllers. The initial recognized controller was an official X-Box product, whereas the second was a GameStop brand knockoff. I don't think this would affect anything, however, full disclosure.
1. I held the X-Box button on the unrecognized controller to take me back to Steam. Because Steam recognized this input, it was the only button I could use on that device.
2. I exited the game and restarted it using that same controller.
3. Once in the game, I held two buttons down to enter the controller setup. Then, I held down two buttons on the first (originally recognized) controller. Both worked!
4. I entered button choices as usual and played two-player for the first time (and had my best fighting game experience in a long time... my friend's, too.)
Controller Input Issues
* I noticed that the control sticks and triggers both have the ability to read the pressure of the button press (the further/harder you press can trigger different actions, like walking to running in other games).
* When I made the left control stick my character movement input, it was way less responsive than the D-Pad (my ultimate choice).
* Both the control stick and triggers could sometimes register input when I didn't want them too.
* For example, when setting up a controller, the sequence has you enter your preferred OPTION key after choosing your R2 button (a trigger). When I first did this, it automatically registered the R2 as my OPTION key, after just pressing it for R2 because it was still detecting an input.
* Similar with the control stick, it made it almost impossible to get a Yomi Counter (I confirmed this in Practice Mode numerous times) because the control stick was still registering input, even if i wasn't touching it. Once changing movement controls to the D-Pad, that problem was solved, too.