I can confirm this issue still exists .
NUC D54250WYK 0025 BIOS
Ubuntu 13.10
nuvoton-cir.ko from 3.11.0-19 kernel
Logitech Harmony Ultimate
The workaround as others have stated is to simply reload the module. For Ubuntu you can put the following script in /etc/rc2.d to have it run automatically at boot.
#!/bin/sh modprobe -r nuvoton-cir echo "auto" > "/sys/bus/acpi/devices/NTN0530:00/physical_node/resources" modprobe nuvoton-cir