Microsoft XML Diff Patch Tool Errors

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I am having two problems with the XML Diff and Patch Tool. The first problem is that the Diff tool throws an error after it tries to read the two files I am having it compare. Apparently it doesnt like my doctype decelerations in the
those files:
Unexpected DTD declaration. Line 2, position 3.
Here is the doctype declaration:
<!DOCTYPE plist PUBLIC "-//Apple//DTD PLIST 1.0//EN" "http://www.apple.com/DTDs/PropertyList-1.0.dtd
Note I do have the setting IgnoreDtd option set for the diff object I am using.

Also I want to read the file created after calling the compare() function. However, when I do this I get an IO exception that says :
"The process cannot access the file C:UsersAdministratorDesktopTesting iPCU TestAPPdiff.xml because it is being used by another process."
This is probably because my diff object still has a process using the file. I need to find a way to kill that process so I can start reading the newly created file. I have been searching through forums and documentation to find anything useful that can help.
If anyone has any knowledge of the diff tool that may be able to help me it would be greatly appreciated. Thank you for your responses.
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