Core: Fix unconditional disarming of timerfd

Core: Fix unconditional disarming of timerfd

* Existing code appears disarms the timerfd always, which cancels
  pending timeouts as soon as one packet completes.
* This fix moves the disarming of the timerfd to
  arm_timerfd_for_next_timeout(), where it is now done conditionally.
  It also avoids calling disarm outside of the above call.
* This patch also ensures that all handling of the timerfd is done
  under the flying transfers lock.
* Issue reported by Hans de Goede. For more info, see:
  https://sourceforge.net/mailarchive/message.php?msg_id=29442693