I wonder if it's also worth a look at the somewhat misguidedly overridden toString() method in SAXException, which has tripped me up from time to time. This example class shows how wrapping an exception in a SAXException can produce a mangled stack trace, containing the class name and message from the nested exception, but the stack trace of the SAXException.

I realise a comment in your blog is hardly the best place to report this problem. I intended to write a comment to the effect of "it would be nice if SAXException didn't produce broken stack traces", but then I realised I couldn't remember exactly how it was broken, so I ended up firing up Eclipse to get my head around the problem again. Is that mailing list you linked to the best place to ask, or is this a known issue that would be redundant?