The icon is generated from stellarium.png. However the current "convert" seems to extract the layers incorrectly. Maybe just use icon.bmp or pregenerate the icon and check it in into CVS.
I has open bug #1617536 on the upstream bug tracking system. I assume, that the problem may raised by the size of the icon, which is 64x64. I assume, that this problem may not raise with a 32x32 icon. Using the icon.bmp file didn't worked.
I have take the icon.bmp file and convert the size to 32x32. This should works correctly.