I ran in to a problem using MakeTran.exe where the upper left corner was not being read properly. A small square of background was left showing. I actually editted the mask.dat to attempt to repair the problem.
Then I happened to notice that my network info tool (Penguinbyte's QuickID) was the same size and "stay on top" in the upper left corner of my screen. I ignore it most of the time and so didn't even notice it ws interferring with my image.
Apparently MakeTran reads the actual screenshot of your image on the monitor.
So I thought I would mention this for anyone who is making skins and has trouble with transparency. Maybe it's obvious to everyone else, but it stumped me for three hours.
HTH, Bill
