Inkscape can also be used to convert PDF to SVG. It's actually remarkably good at this, and although the code that it generates is a bit bloated, at the very least, it doesn't seem to have the particular issue that you are encountering in your program. I think it would be challenging to integrate it directly into Java, but inkscape provides a convenient command-line interface to this functionality, so probably the easiest way to access it would be via a system call.
To use Inkscape's command-line interface to convert a PDF to an SVG, use:
inkscape -l out.svg in.pdf
Which you can then probably call using:
Runtime.getRuntime().exec("inkscape -l out.svg in.pdf")
http://download.oracle.com/javase/1.4.2/docs/api/java/lang/Runtime.html#exec%28java.lang.String%29
I think exec() is synchronous and only returns after the process completes (although I'm not 100% sure on that), so you shoudl be able to just read "out.svg" after that. In any case, Googling "java system call" will yield more info on how to do that part correctly.
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