When you were testing out your own "greyed" icons, I think I know why you only saw little black boxes. You probably did not save at a high enough bit/pixel rate. It is best to save files with transparencies at 32 bit/pixel setting, otherwise SH3 cannot read it and will display odd things.
Either that or Infranview did not work correctly. Also, I have no idea why PS cannot access those unit icons, which is really weird because GIMP can...
