Fixed...
For some reason, having the .dat file in my WEB-INF was altering it significantly. The MD5 checksum was not the same.
Taking it one root above to my "webapp" folder which housed WEB-INF somehow escaped the changing of the file and the MD5 validated...
Might have to file a bug with Google for this one, or I'm misunderstanding something entirely...
UPDATE: Upon further introspection I've decided that it might of been the text set that my WEB-INF was using... UTF-8. This is the only thing I can think of.