Steve, have you checked the max_trace_level setting in global_settings? 
I'm 99% sure this is your problem, since the default max_trace_level is 
five. If it's set too low you will get opaque effects (usually black).

Try this at the top of your scene file:

global_settings{
  max_trace_level 10
}

Keep bumping it up until the black opaque areas are vanquished.

Hope this helps.

-Samuel Benge

Steve Shelby wrote:

> The images are of a series of thin translucent boxes with small spaces
> between each. The effect of added opacity for each added layer is realistic,
> until it gets to the fifth layer, where the completely opaque dark
> rectangles appear. <snip>
>

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