I have noticed that if I enter the header/footer and insert text then move to the body of the document and insert a table the width property is not respected. It seems that the table property “preferred width” is set to 100%. I have no problems with the tables if I stay out of the header/footer.
Please attach an example of your code and original document template. We need to have a look at it.
Please make sure you use the latest hotfix of Aspose.Word.dll as I remember a similar issue was fixed recently.