Transparent areas in graphs gone when imported into Powerpoint

I am a research scientist in the area of molecular endocrinology at the National Institutes of Health. I have been composing slides on Powerpoint that contain graphs, text, and graphics, all on a background that is constant for all slides and shows through everything but the actual graph itself. I have been doing this by using KaleidaGraph 4.03 to make the graph (complete with curve fitting, colored bars or points, and x- and y-axis legends), pasting this into ClarisDraw 1.0v3 (still one of the best programs for Mac ever invented) to add additional text and graphics, and then pasting all of this into Powerpoint (Office X; Office 2004 does not work as well), on either a Mac G5 or G4 laptop using OS10.4.9 (NOTE: to get a nice clear paste, you have to use “multilayer selection” and “select all” but then deselect one unnecessary item, otherwise much of the text comes through pixilated). However, my days of being able to use ClarisDraw are limited so I have been using an OS10 graphing program called Intaglio 2.9.3, which also allows nice conversion of previous ClarisDraw files. The problem is that with Intaglio, everything that is exported to Powerpoint has a white background instead of letting the background of the Powerpoint slide show through around the text and graphics. I have talked to the people at Intaglio and they say that the problem is mainly that Microsoft Office currently only supports Apple's graphics formats from Mac OS 9 and earlier, specifically QuickDraw graphics, which Apple considers obsolete and has replaced with Quartz. Ideally PowerPoint should allow the use of PDF as the graphics import format since that's what Apple has standardized on for Mac OS X, but it doesn't. Does anybody know a work-around? Failing that, how do we persuade Microsoft to allow more recent Apple graphic formats?
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