I'll update as soon as I'm home from work!
I've updated Brilliant Diamond's codes to v1.1.2, but am waiting on the new encounter address for Shining Pearl before I can update it as well. The download has been updated, and as soon as I have the new address, I'll include v1.1.2 codes for Shining...
Are you on v1.1.1? Are you using the [Encounter (ON)] code with it?
That code already exists but it currently needs to be fixed as it'll cause a white screen around 80% of the time during my testing of it. Here's the code as it's been posted;
[Encounter Pokedex number]
There's no Azure Flute in the files for BD/SP right now.
Only way to get Arceus is to use PKHeX or use the encounter code. There's no event for Arceus in the game at the moment so there's no way to trigger one.
You have Arceus's and Manaphy's Encounter Codes included in the .txt for Brilliant Diamond/Shining Pearl; here's the encounter codes for Celebi and Deoxy's as currently AFAIK there's no possible way in-game to obtain them as well without using these codes.
Brilliant Diamond v1.1.1...