The only thing I can come up with is that the overlay flag is on. This changes any black pixels into a fully transparent pixel. To fix this, you have two options:
1. Turn the overlay flag off (has to be done via script - my.overlay = off; in an action).
2. Change all black areas into something that isn't black. For a 24 or 32-bit texture, the closest to black is the color 000001, the absolute darkest blue and blue is the darkest of all colors. For a 16-bit texture, use 000008 (set blue to 8 with the others at zeros).