Please make sure that in Aperture Preferences > Previews you have set "Share XML…" to "Always"
Aperture then creates a file listing the contents of the library. This is what HoudahGeo works from.
Aperture usually writes / updates the ApertureData.xml file as you quit the application.
Aperture also has to create the image previews that are listed in the ApertureData.xml. This can take some time.
Check if the file exist and is current. Right-click your Aperture library in Finder and select Show Package Contents from the context menu. The ApertureData.xml should be right there at the top level of the library package. You can use a text editor (e.g. BBEdit or TextMate) to take a peek at the contents of the file. Check if the missing images are listed.
If you find the file to be out of date or incomplete: quit Aperture, trash the ApertureData.xml, return to Aperture and make a change (e.g. import a new image) and quit Aperture. It will write a fresh file.