You can't import images directly into organizer from a usb thumb drive, then remove the thumb drive. Once organizer gets the original location of the images you cant change their location without first telling organizer.
Itotally jacked things up about a year ago: I was moving thousands of images around and not thinking about how it would affect organizer. Once things got all situated I just deleted the various catalogues, and started over. I dont spend alot of time editing the image meta data- but many do.