I am having a problem with Cryptomatte. Everything works great until you go back into a project. When you go back in, each layer enhancement using crypto loses its Cryptomatte power and applies the tweak to the whole scene.
What image format are you using for an output? I can’t reproduce it with a multichannel .exr. Or are you talking about when opening and re-rendering the same scene? Have you used DR by any chance? Does it get fixed if you hide/unhide the masked layer?