Not sure what the "correct" behavior here is, but archetypes adds the pom in the directory it's run from as the parent, this might be a good idea for pax:wrap aswell.
This isn't a bug:
1) if you run pax-wrap inside a pax-construct project it will use the generic wrapping pom as the parent (ie. poms/wrappers/pom.xml)
2) the default parent for poms without a parent is already ../pom.xml
3) if you want to force it to use a different parent pom the you can use the "-DparentId=groupId:artifactId" option (http://www.ops4j.org/projects/pax/construct/help/wrap-jar.html)
BTW, there are a lot of benefits from using a parent pom that's different from the one in the directory above - for example, it means you can have modules that use different configurations for the same plugin (in this case the bundleplugin) underneath the same modules directory. This isn't possible if you always use the pom directly above you as your parent.