Upscale changed black to transparent

[Kupo91]

I upscaled like 100 alpha layers. And they actually look all very similar. But there must be something different between some of them, because ~50% of these textures lost their black color during upscale process. In windows explorer they were full white, in gimp they had transparent background instead.

First one texture which upscaled as intended:

Original:

Upscale:

And now a texture which had this failure:

Original:

Upscale:

I attach the files and the log from this session: files and log.zip