Hi Ryan,
What that means is that the PNG's that give you that issue are saved as 24 bit PNG's with no alpha channel. By setting the alpha to 99.9% you are forcing it to be rendered as if there was an alpha channel.
Materials with no alpha will actually get rendered in a different order from objects with an alpha channel, so it is probably disappearing behind some other object in your scene. Your workaround of using 99.9% is a good option; the other option is to export them as 32bit PNG's instead of 24 bit.
#XPression