Thanks @cameron-fmod, reading that documentation gave me the idea to check the initialization order of the FMOD Studio plugin and the first time GameplayCueNotify assets are loaded from disk at startup. I found that the default loading behavior for GameplayCueNotify assets is async, which explains what I was seeing in my debugging. I was able to fix the issue by overriding ShouldSyncLoadRuntimeObjectLibraries and ShouldAsyncLoadRuntimeObjectLibraries in our project’s GameplayCueManager subclass so that when in the Editor, Gameplay Cues are loaded synchronously.
I’m not really sure how the FMOD Studio plugin could account for this, but it seems to be the case that as of UE 5.5.3 the AssetRegistry hook being used to reload banks at startup is not accounting for async loads still in progress.