How am i supposed to make an alpha??

I have been having a very annoying problem with my texture in the game engine. No one seems to know how to fix so i decided to ask how to prepare a texture and how i do it now, maybe that will help.First my problem when i add my object in my game that uses alpha
some look normal others transparent Does not make sense they are the same object. . No one has been able to fix so i am assuming i am do it correctly. This is how i prepare my texture In GIMP i add a transparency layer around the entire picture and on certain sections of the image i lower the opacity to about 50% because i need an onion skin look to it. (this only happens when using alpha)
then i save as a png. Is there another way to do this? do you need my texture as an example to look at? I need to fix this problem once and for all

digiman