Partially missing colours in pdfs

Hi, I'm trying to create some pdfs by using Acrobat 7 (on Windows XP) as a printer (which I am selecting in the program I'm using, a drill hole cross section plotter called Interdex). The printers in my office don't have ARCH E size paper, Adobe does, and I need to make these big enough to plot on large, plotter-style printers.
The problem I'm having involves the colours in the drill holes. At some point, approximately 2/3 of the way across the section, the colours disappear. If you're unfamiliar with drill-hole cross sections, imagine a histogram, turned upside down, where the bars are multicoloured, and on angles. The colours (representing rock types underground) disappear suddenly: one bar has colour at the top, but nothing at the bottom. The line where colour ends is sharp, and perfectly vertical (even though the bar is on a 60 degree angle).
It's not the colours themselves, because all of the missing colours are present elsewhere on the section. It's not that the pdf loses all colour at a certain point, because there is a legend, in colour, past the boundaries of the cross section. If I use a different paper size, there's no problem, but I need to use ARCH E to get the proper scale.
I've attached a very very rough example of the problem. Notice that the colours stop halfway down hole number 3, and that hole number 4 has no colours at all, even though both should be completely filled. The black lines should always be visible, but my hands not that steady when I'm in a hurry. They stay visible, exactly as shown, even when the colours are missing. They represent downhole traces, basically a vector indicating direction and depth of the hole (they are not related to the colours). Text associated with the holes is also unaffacted (e.g., the 4).
Are there known issues using Adobe as a printer, or with certain paper sizes? Any help would be greatly appreciated.

If your client wants local copies, he can right-click on the link
offering the pdf. It will give him the option of saving to his computer.
Mike

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