Your after document's heading 1 style definition includes numbering (<w:numId w:val="3"/>):
Using xml Syntax Highlighting
<w:style w:type="paragraph" w:styleId="Heading1">
<w:name w:val="heading 1"/>
<w:basedOn w:val="Normal"/>
<w:next w:val="Normal"/>
<w:link w:val="Heading1Char"/>
<w:uiPriority w:val="9"/>
<w:qFormat/>
<w:pPr>
<w:keepNext/>
<w:keepLines/>
<w:numPr>
<w:numId w:val="3"/>
</w:numPr>
<w:spacing w:before="480" w:after="0"/>
<w:outlineLvl w:val="0"/>
</w:pPr>
Parsed in 0.002 seconds, using
GeSHi 1.0.8.4
So the numbering is to be expected.
Your before docx does not have a definition for heading 1, so when you use it, docx4j falls back to use the entry from:
org/docx4j/openpackaging/parts/WordprocessingML/KnownStyles.xml
defined as above. (As an aside, I noticed that the addStyledParagraphOfText method didn't cause a Numbering part to be added. I must confess I never use this method myself...)
So to avoid this behaviour you should ensure the style is defined in your before document. In practice, this happens if in Word you use the style in the docx.
Alternatively, you can programmatically add the style.
Or you could change the definition of the style in KnownStyles.xml