ptab: as it says, there is currently no support for the ptab element. Its not commonly used. You can either remove it from your docx, or we could look at adding support for it to docx4j.
altChunk: these need to be preprocessed into "real" docx content for docx4j's PDF output. If the altChunk is of type XHTML, docx4j can do that. If it is a docx altChunk, the Enterprise Edition is required. There are other types of altChunks, which you should avoid if you want to convert to PDF...