I just tried to reproduce this without success. Here's what I did:
1- Create scene "1.unity" with a Cube and a Sphere.
2- Add an AkAmbient and an AkBank to the Cube, set to play on start
3- Create scene "2.unity" with a Capsule
4- Add an AkAmbient and an AkBank to the Capsule, set to play on start
5- Write a script that sets DontDestroyOnLoad to true on a GameObject, and attach it to the Cube and the Sphere in scene 1.
6- Write a script that calls SetActive(false) on the Cube and then loads scene 2, in the OnMouseDown function. Attach it to the sphere.
Now, when I preview the game in the Editor, I hear my first sound. When I click the Sphere, the Cube disappears, but its sound continues to play. The capsule appears, and its associated sound begins. No error messages are printed in the console.
Is this similar to what you are doing?