I created a new Survival mode Single-Player map with Bonus Chest On and Allow Cheats On (World Type: Default, Generate Structure: On; no seed).

A new 13w36a world was generated and right after spawning, I looked for the bonus chest nearby and couldn't find it. Instead I found all the items from the bonus chest underwater in a nearby water hole.

I've re-created the world with bonus chest (Seed for the World Generator was 5360052084810066501) and successfully duplicated the issue. (Bonus chest items continue to spawn underwater.)

*What I expect to happen was to see the chest on solid ground (land) - not underwater.

*What actually happened was the items from the chest were spilled out at the bottom of a 1x deep water pool.

Steps to Reproduce:
1. Create a new Survival 13w36a world with Seed: 5360052084810066501
2. Set Bonus Chest On, Cheats On, World Type: Default, Generate Structures On.
3. Start/Spawn in-game