How are you doing the conversion? There are several methods with LaTeX and it may very with method.
Sorry for the late reply
Postscript to PDF
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I am not sure, but I suspect some sort of transparency. Graphics is not my strong suit, but transparency may be the issue. Also, a lot may depend on the structure of the PS file you are using. You might try GSView or the PDF creater in your LaTeX distribution (most have one).
OK, I will check and let you know