You can see what I mean with this example.
png source file:

pdf result:
http://www.impressusart.com/stuff/test.pdf
I've tried on multiple files and formats as the source file (png, bmp, tif). The only one it doesn't do this with is jpg.
This happens with different versions of both ghostscript (is that used here?) and imagemagick.
This is not a transparency issue, because I tried exporting to bmp and it still did it, and there's actually no transparency in this file (no transparent or partially transparent pixels). Even if it were, this darkening and color change wouldn't make sense.
What am I missing? I've googled for hours about this, and nothing I can find addresses this issue. Thanks.