While experimenting with UIMA I observed a problem similar to the one already posted here: http://tinyurl.com/32spzv9. Since removing Saxon from the classpath was not an option, I found the problem to be the way namespaces are handled in org.apache.uima.cas.impl.XmiCasSerializer$XmiCasDocSerializer.
First of all, the addAttribute/3 method was incorrectly passing null as uri and localName parameters. According to the javadoc, these must at least be empty strings. I added a hack to extract the localName from the qName, if available.
Second, the method computeNamespaceDeclarationAttrs/1 only added namespaces as attributes, which are not honored by Saxon. I think this is correct, as the SAX2 standard states that namespaces must be declared via startPrefixMapping/2, so I added that, as well.
Attached you find a patch with changes which work for me (and seem to solve the problem).