My remote sometimes required pi3 reboot to work again.
Found same problem on April and June release.
Fix for usb xbox ir receiver not working sometimes on boot.
installed usbutils:
apt-get install usbutils
found working usb dongle:
Port 5: Dev 4, If 0, Class=Xbox, Driver=lirc_xbox, 12M
found not working usb dongle:
Port 5: Dev 4, If 0, Class=Xbox, Driver=xpad, 12M
fix was to diable xpad.
edit:
/etc/modprobe.d/fbdev-blacklist.conf
add:
blacklist xpad