I did a little research on the forums, and it looks like ZEN Apps are
supposed to use 256 (or less) colors and 32x32 size.

My NAL apps use 256 color 32x32 icons, with the background set to be
transparent so it looks pretty in NALWin and NalExploder.

However, we are looking to begin using the webified version of NAL
(myapps.html) for our users.

The problem is, the icons in myapps.html are either completely black or
mostly black in most cases. If I remove the transparent background and
knock it down to 16 colors, it looks OK (but pretty ugly), and the
background sometimes clashes with the myapps.html background.

Is there a fix or a workaround I am not aware of?

Using ZEN 6.5 SP1.