Not sure if necro..but what the hay:

1) Assuming you have unlocked diving in Stormblood (part of the main story)
2) rebind it somewhere else, without ctrl, to see if it works. Like the “v” key.
3) Does your keyboard have sticky keys/ghosting issues (too many keys at once = irnogred keypresses). Check that.
4) make sure you are trying to dive in open water and not shallow pond/coast

Good luck!