I've always used the magic wand tool the select all the white and delete it, sometimes you have to mess with edge selection by growing or feathering the selection.
Using a targa gets rid of this. It's the way Photoshop saves PNG files. Any transparent pixels have their colour removed and replaced with white. Select the opaque pixels and make a new alpha channel, then set those opaque pixels to white. Save as 32 bit targa and forget that PNG even exists.
I got it, I was messing with the layers in a wrong way that it kept messing up. It was one of those tiny little things you keep glazing over. Thanks ZacD, you got me to relook in an area. I basically shrunk the selection by one pixel, and deleted it, but on another layer I still had the original space there. So I didn't…