When using Beta 2.1 of Shutter Stream and Canon cameras, the software will not always open on El Capitan.
Unfortunately, the issue has to do with Canon's SDK. At the moment, Canon does not have an El Capitan compatible SDK.
From our own internal testing on El Capitan, we've noticed that if we used their old x64 SDK, then sometimes things start up and sometimes they don't. At this point you have the following options:
1. Keep trying to restart the program and as you've noticed: sometimes it works, sometimes it doesn't. The issue here is that the Canon SDK fails at initialization.
2. Use the software with a compatible Nikon camera. Nikon has provided to us the El Capitan version of the SDK and that's worked well with Shutter Stream 2.1.
3. Rollback your Mac OS to anything before El Capitan. In that case, I would also recommend that you switch to ShutterStream 2.0, since 2.1 is beta.
4. Switch to a Windows machine.