Yep,
In this case the problem at least is that your GeoTagger does not write into the original file but only to an xmp sidecar file. Aperture on the other hand only recognises the GPS info embedded into the actual file; it knows nothing of xmp sidecar files (an Adobe invention anyway). There are two fixes for this problem: either HoudahGeo starts to support embedding GPS data into the RAW file (like PM does actually) or Aperture starts to recognize xmp files.
This latter solution not being very likely as xmp sidecar files are an Adobe invention and see little support in other software (PM is a good exception though).
Hmm, perhaps by forcing PM to update IPTC/XMP data (e.g., by "changing" a field to its own value), PM will embed the GPS data as well from the xmp file (as long as you've correctly set your xmp/iptc preferences, this certainly works for that part of the metadata, I'm just not sure about the GPS part. Certainly worth a try though).
Cheers,
Hayo