I now have a workaround for this problem. Although it would be a much nicer and cleaner solution if Unity would rely on an official released fmodex.dll.

The workaround is to delayLoad the fmodex.dll from your own dll. To do this you need to set a special linker option when building your dll. This alone won't save you, it will still throw the exception the first time you make a call to an fmod function.

To prevent that you have to specify a "delayHook" (http://msdn.microsoft.com/en-us/library/f0fkfy9y.aspx). In our case we only need to handle the "dliNotePreLoadLibrary" case and reroute the call to fmodex.dll to someothername.dll. Now we can include a renamed fmodex.dll (using the specific release that you linked your dll against) in our project root folder. When we start the editor it will try to load fmodex.dll the first time we make a call to any fmod function. Instead trying to load the unity fmodex.dll it will now load the correct dll. Here's the example code for the delayHook function.

FARPROC WINAPI delayHook( unsigned dliNotify, PDelayLoadInfo pdli )
{
  switch( dliNotify )
  {
  case dliNotePreLoadLibrary:
    if( strcmp( pdli->szDll, "fmodex.dll" ) == 0 )
      return (FARPROC)LoadLibrary( "fmodex2.dll" );
    break;
  default:
    return NULL;
  }

  return NULL;
}

To actually use this hook you have to include this line of code on a global scope within your dll:

PfnDliHook __pfnDliNotifyHook2 = delayHook;

I hope this helps someone with a similar problem, as it took me way too long to figure this out...

I had the same problem and solved it by renaming my version of FModEx.dll to FModE2.dll and changing every occurrence of that name inside both dlls, Ex and Event, with a Hex Editor.

A better description of this answer is also on this link:

http://answers.unity3d.com/questions/2786/dll-loading-in-editor-on-windows/3920#3920

Just stumbled upon this problem, too.

Is there a better solution than using two different FMOD builds at once?

Even if the internal verison is custom built: Is the internal FMOD not fully accessible?

Can you describe "not working" in more detail? (Unity won't start? crashes? ) Unity is using a custom build of fmod (based on 4.26), so using another vanilla (even 4.26) version of fmod could lead to a undefined behaviour. But if your not using AudioSource/Clips at all and only fmod::channels/sounds you should be fine (using 4.26). But again, I need some more details on the specific errors.