When trying to modify a HEADER or FOOTER record using poi on a sheet that contains embedded objects (such as charts) and the embedded object contains a HEADER or FOOTER record (such as charts) you are actually modifying the HEADER or FOOTER of the embedded object.
Created attachment 7195 [details] simply change to make sure HEADER we get belongs to the Sheet and not an embedded chart
This patch seems to have some unintended changes to buid.xml and .classpath.
Applied the pertinent part of the patch to fix the problem. Created a test case that first found the problem and then passed when the patch is added. BTW, I removed the entries to build.xml and .classpath from the patch.