Hi,
You might have noticed Ship Sim Extremes only takes into account the two first joysticks identified by windows (#1 and #2). If you own more than two joystick, that may lead to problems (for example if you want to use the joysticks #2 and #3). And this order can change after a restart, or if you've plugged/unplugged joysticks.
I've found a useful and free software, which allows you to manually define the joysticks ids. You just have to launch this software prior to starting SSE, to set the joysticks you want to use as #1 and #2.
This software is called JoyID, and you can download it from here :
http://www.wingmanteam.com/latest_software/gadgets.htm#JoyIDs_Utility: