All I’d like you to do is go into MediaPro, highlight a picture that you’ve assigned to multiple keywords, and choose Action | Extract Metadata… from the menu at the top. Make sure Editable Annotations is checked and then save the resulting XMP file in the directory where the image resides.
Finally, try to import the XMP and/or image file into Aperture, either by dragging/dropping or through any import mechanisms it may have. I’d like to know whether Aperture retains the keyword (and other) metadata. Thanks in advance.