If Kirrkenwing has Tough 1 or Tough 3, when it uses the Shimmering Wings ability, it gains Tough 2 once the effect comes to an end. I believe this is because when the rune was originally made, Tough was not an upgrade option. As such, the SW ability was counted as a "group" with Tough, so my guess would be SW is coded to remove Tough then return Tough 2.
And while we're on the subject, I have no idea how to reproduce this but sometimes if you activate Shimmering Wings while the champ is moving (I do it by pressing 2 if that matters), it will not activate and the ability will go on cooldown.