I just purchased HoudahGeo (HG) to use its KML export features and just upgraded to Aperture 3. I have been scratching my head for awhile trying to figure out why Aperture was not showing that the location of the photos I had tagged using HG. Luckily I found this thread and finally had some success.
I was having the same problem described earlier in this thread. I was simply selecting photos from within Aperture and then dragged them to the HG gui and dropping them to be loaded into the active project. I would then geocode them and export to EXIF, execute the Update Masters command, only to find the location was not being written to the masters.
After reading this thread I used the Reveal in Finder trick and found that HG thought the photos were in the in the previews folder buried in the aperture library.
So I started over this time, using the finder interface to select the files. After exporting and using the Update Masters command in Aperture everything worked perfectly.