
Paint.NET:
Transparency is saved correctly, header is always saved wrong.
GIMP:
Transparency is saved correctly, header is preserved from already existing file (do not fix wrong one) or if the new file is created by GIMP, correct header is appended.
ImageMagick:
Preserves header (do not fix wrong one).
XnView:
Fixes and writes correct header.
IrfanView:
Fixes and writes correct header.
ArtGem:
Always writes wrong header. Transparency is saved correctly.
Painter X:
Transparency and header are saved correctly.
Photoshop CS4:
Always writes wrong header. Didn't know any convenient way to get semi transparent images working.
Addtional notes:
Fixtrans seems to mess RGB color space. It is seen both in XnView and Painter X.
RGB color space in Painter X:

RGB color space after fixtrans'ed conversion:

Need to look at it deeper, though.