not sure if it helps, but please /proc/ioports below. There is a
difference between kernel 4.13 (not working) and kernel 4.5.7 (working):

kernel 4.5.7 (working):
  0220-022e : nuvoton-cir
  02e0-02ee : nuvoton-cir

kernel 4.13 before suspend and before module reload (not working):
  03e0-03ee : nuvoton-cir
  0a20-0a2e : nuvoton-cir-wake

kernel 4.13 after suspend and module reload (working):
  0220-022e : nuvoton-cir-wake
  02e0-02ee : nuvoton-cir

Maybe resource allocation is causing issues here....

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https://bugs.launchpad.net/bugs/1730958

Title:
  nuvoton-cir not working after boot

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