plutext/docx4j — pull request #34 by jlesquembre (2012-10-29 13:21:34+00:00)
Title: Header and footer keep the layout as applied after PDF conversion

More info:

https://github.com/plutext/docx4j/pull/33
http://www.docx4java.org/forums/docx-java-f6/issues-after-using-the-latest-nightly-build-t1232.html

This should solve the first problem of the post.
The other issues have another cause, I think. Or at least I cannot see how this code can cause these problems