Hi Morten,
I keep my keywords HUD locked to avoid “keyword pollution” via Photo Stream and other imports. A side effect of this is when using the Convert Master script, I wind up with an “Imported Keywords” section of keywords.
I made modifications to the script to avoid this (deltas posted at http://sdaven.blogspot.com/2013/05/convert-aperture-originals.html). Sharing here in case you're interested in incorporating the changes.
Thx,
-scott