Kiora triggers off of having a certain number of mana gems.
She seems to count fragile mana gems produced by Birds of Paradise as well as the fragile mana gem you get from playing second, but she doesnt count the fragile mana gems produced by the Mana Short trap.

I do not have a Gaea's Cradle so I can't test if that works or not but this seems inconsistent.

The steps to reproduce are fairly simple. get to 9 mana, play BoP and watch her trigger then get to 13 mana and play mana short where your opponent leaves empty mana open.