After a bit of digging, you're right! Some effects are deepfrying the texture, which is causing the darkening. Will be patching it in the next update.
You'll also be happy to know I'm working on better palettization options (Median Cut, K-Mean) to get better PS1 style palettization, and looking into improving the PSX shader.
And all good. Hearing the pain points helps make the tool better, so your feedback is greatly appreciated! Thanks again! 👍