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The expected results for these test cases have extraneous whitespace and eol characters at the end of the files.
Is maybe fixed in CVS. I don't think this was whitespace. XML may have whitespace after and before the document element since it is redundant to the XML c14n, and many other tests have such whitespace. However, these two baselines had XML comments, which I suspect is what the code is triggering on. Feel free to verify.
Apologies, the problem was with my test harness and not with the expected results. When I saw a scenario of runtime-error, I did not look further to see if a non-error result would be acceptable.
I've returned the expected results back to their previous states in CVS.