I got into a discussion with someone over an issue that spiraled into a mild argument, after she was done saying what her "pet peeve" was she finally listened to what I said to fix her issue. What was the issue you ask?
She bought a pair of jeans that had Sculptie pants legs and saw the alpha texture as "see through" I've had that issue myself along with others who have purchased shoes or clothing with alpha textures on them.
There is a very simple solution that I found on my own, couldn't find it through the SL forums so decided to search the interface for myself.
When your seeing Alpha Textures as missing or see through try this;
Activate the "Advanced" menu with Ctrl-Alt-D, or Opt-Ctrl-D on a Mac.
Check Fast Alpha (If it doesn't have a x next to it, click it!)
That should solve a few issues with alpha textures missing and see through, I'm not sure if Viewer 2.0 and other viewers have fast alpha cause I only use Phoenix, So just try it out and see if it works for you!