Environment: Windows, RPG Maker MZ 1.9.0, RPG Maker Cook Tool Deluxe 6.1.4.
Unchecking the following two options makes APNG work, but that defeats the purpose of packaging:
Asset Preparation's “Encrypt assets” and “Source code protection”.
Please update RPG Maker Cook Tool Deluxe so it works correctly without needing to uncheck these options.