Yes, this is does look to be a bug. Here is the RTF output (which is more accurate for figuring what Scrivener alone does, since .docx adds the complication of the Java-based third-party conversion engine), as examined in Nisus Writer Pro’s sidebar where a section’s page numbering is established:
[size=80]Left: result from Scrivener 2.9; Right: result from 3.0.1[/size]
Here is the section break and header reconfiguration in the 2.9 RTF:
[code]\b\fs36 \cf0 \sect\sectd
\pgnlcrm\pgrestart\pgnstarts1{\footer {\pard\qc {\f0 \fs32 {\chpgn}\b0 \i0 \ul0 \par}}}
[/code]
And in 3.0.1:
[code]{\keepn \f0\fs48 \cf2 \sect\sectd
\pgndec\pgncont{\header {}}
{\footer {\pard\qc {\f2 \fs24 {\chpgn}\b0 \i0 \ul0 \par}}}
[/code]