As the title suggests, when I have a gamepad connected (in this case, a direct-X controller, configured with x360-ce), the input is only recognized for a second player. If I select to have 2 players, then only the second player-controller receives input from the gamepad. If I select 1 player, then no gamepad input is received at all. The controller works fine when navigating the viewport before entering PIE.
EDIT: After further investigation, I found that it specifically is diverting the input to the second instance created by the PIE, and not simply the second player-controller.
EDIT 2: Never mind that previous edit (annoyingly, there is no strikethrough markdown support on here); I found a solution. In my pawn class, on begin play, I took the player controller from player index 0, and set the player controller id to 1. This seems to have worked. I will keep this question open, since I am still unsure as to why this workaround is necessary, and would like to solve this in the most proper way possible.
