So, I was battling against someone's Skarmory and every second turn it only took the steel typing into account when doing damage calculations.
I had Cloyster out, I used Icicle Spear, regularly effective.
They used Stealth Rock.
I used Icicle Spear again, but this time it was not very effective. (And I did check, it did half the damage that it did the last time)
Later, his Skarmory (Back at 100% after a roost) was out against my Breloom, I used Substitute.
He set up some Spikes.
I used Focus Punch, they set up some more spikes while I focused, and it hit regularly effective. They had >50% health left.
The second time round, they hit my substitute, and it faded.
And I used Focus Punch, but this time it hit super effectively and took out the Skarmory.
I'm not sure what was going on there. But it appears that the Flying typing wasn't being taken into account.
Sorry I don't have the script from the battle because an update force closed it. Bad timing, I know.