If your alpha areas are all the same color and opacity, here is one way to make the white areas transparent if you have Photoshop (I don't know about other graphics editors):
Create a new image the same size as the texture image, making sure that "transparent" is selected. The new image should look like a checkerboard patern indicating that it is transparent. Select-all on your original texture image and copy. Then paste onto the new transparent checkerboard image. Finally, using the magic wand tool, select the white areas and press delete. This will turn them from white to transparent (which will look "checkerboardy"). Save in the .png format to retain alpha information.
If that isn't your problem (i.e. if your alpha areas are already transparent but still not showing up correctly in jPCT), check a couple of things in your code:
Make sure you use true for the useAlpha parameter when creating your Texture instance:
TextureManager.getInstance().addTexture( "GLOWBALL.PNG",
new Texture( getClass().getClassLoader().
getResourceAsStream( "Textures/GlowBall.png" ),
true ) );
Play around with the int parameter for setTransparency:
glowBall.setTransparency( 0 );
Depending on what you are using the texture for, you may want to change the transparency mode or eliminate external lighting:
glowBall.setTransparencyMode( Object3D.TRANSPARENCY_MODE_ADD ); ...for example...
glowBall.setLighting( Object3D.LIGHTING_NO_LIGHTS );
glowBall.setAdditionalColor( ...whatever... );
--EDIT--
Another way if there is only one single transparent color in your texture, then change that color to black (color 0,0,0), and use a higher number int parameter for the setTransparency method (say 100 or so). In this case, you would want to use false for the useAlpha parameter when creating your Texture instance. If there are other black places in your texture, make sure they are a "different" black (say color 5, 5, 5 or something).