This seems to be new with the current beta on Steam.
Steps to reproduce:
-Make an ase file with a single normal layer, indexed colors, with the first color set as the transparency color. Fill the field with that transparent color.
-Draw something on the canvas with some other color.
-Save As > save this as a GIF file. The resulting GIF file will have lost its transparency.
If you open the new file, you will find its palette has been changed, with black colors added until index 63, and the new background color added as 64th color in the palette.
If you select that color and delete it from the palette, then save the file again, transparency is restored.
Expected behavior: The saved gif should keep its transparency.