When you save to a .gif file (i.e. an animation), bad things happen to a project that contains an effect layer (for example, soft light) on top of another layer.
What is happening behind the scenes, is that colors from the soft layer force a palette adjustment to accommodate colors that result from the overlap of the soft light layer on top of another layer. In an animated file, it can be a lot of colors.
Since the entire palette gets replaced, often one unfortunate color gets shoved into the color 0 slot. The program also makes that color transparent in the .gif file palette.
This is undesired.
Known workaround: flatten all layers and pray for an acceptable result.
Expected behavior: if color 0 slot must remain transparent, no used color gets shoved there when creating a new palette. Probably better to “lock out” that color as an option somewhere.