I'm having a similar problem, did you use curl?
This is my syntax and it returns a fault making me unsure if the content-type actually is applied.
curl -i -s -S -k \
-H "Accept:application/*+xml;version=1.5" \
-H "x-vcloud-authorization: ${VCLOUD_AUTH}" \
-H "Content-type: application/vnd.vmware.vcloud.networkConfigSection+xml" \
-X PUT "https://vcloud.test.internal/api/vApp/vapp-e4eedb31-cf3a-4cf2-a676-0ee6e3789d33/networkConfigSection/" \
-d @vapp_vcloud_network.xml