Logic-based mods do not work while skin mods load correctly (Sonic Frontiers 1.42, PC)

I am using Sonic Frontiers on a standard Windows PC (not Steam Deck) with game version 1.42 and the latest version of Hedgehog Mod Manager. Game file integrity is verified with no issues, antivirus and real-time protection are disabled for testing, and both the game and Hedgehog Mod Manager are run as administrator.

Skin-only mods load and function correctly, confirming that basic mod injection is occurring. However, logic-based mods that rely on gameplay, animation, or transformation logic (such as Super Sonic or Shadow mods) do not work correctly. No transformations or gameplay logic changes trigger, and there are no crashes or error messages.

More specifically, when using Shadow, the boost behavior is clearly broken: the boost speed is not properly scaled and behaves incorrectly instead of the expected controlled boost. Additionally, character-specific logic does not seem to apply, as the cyloop remains blue (matching Sonic’s default behavior) instead of turning red as expected for Shadow.

Transformation logic is also affected: pressing Up on the D-Pad while jumping, which should trigger the Super Sonic transformation, does nothing and no transformation occurs

A short video demonstrating these issues is provided below for reference.

https://www.loom.com/share/dfaa23831bb745aa934dda0a4d37c1c2

Reproduce the report with Sonic Frontiers 1.42 on a standard Windows PC using the latest Hedgehog Mod Manager, comparing a working skin mod with the affected logic-based mods. Start with the linked demonstration video and the mod-manager behavior; done means Shadow boost and cyloop behavior work and the Super Sonic transformation triggers as expected.