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It seems like something in Qt or one of the plugins was interrupting the system call I was making to read the joystick input. Adding additional try/catch code to my joystick implementation solved the problem for me, since it can just continue reading input even if it is interrupted. I was also able to get my plugin working without crashing and without the additional try/catch code by adding my plugin to the GUI last, after all the other plugins were loaded and running.
Got the idea from this StackOverflow thread. I'm still not sure what part interrupted my system call, why it did that, or if it's intentional, but the solution seems to be robust to random interruptions on startup.
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