They are probing to see how deep your relationship is and if it's been tempered in the crucible of turmoil, chaos and change.
I would emphasize, if it's true, that you worked together on some great project as either peers or boss/employee. It's also good to mention that, if true, you worked at multiple places together.
The other thing they are trying to glean is if you complement each other's skill sets and together make a stronger team.
Startups are all about getting stuff done quickly and efficiently while having a ton of fun. At times, it's crazy nuts and people that know each other well understand how to motivate each other through tough times.
It's kind of like remodeling your house. At some point, you will turn to your partner and say "why the heck did we do this?" and hopefully, they reply "because dear, think how wonderful it will look when it's done!"