“Content is not allowed in prolog” when parsing perfectly valid XML on GAE

The encoding in your XML and XSD (or DTD) are different.
XML file header: <?xml version='1.0' encoding='utf-8'?>
XSD file header: <?xml version='1.0' encoding='utf-16'?>

Another possible scenario that causes this is when anything comes before the XML document type declaration. i.e you might have something like this in the buffer:

helloworld<?xml version="1.0" encoding="utf-8"?>  

or even a space or special character.

There are some special characters called byte order markers that could be in the buffer. Before passing the buffer to the Parser do this…

String xml = "<?xml ...";
xml = xml.trim().replaceFirst("^([\\W]+)<","<");