RAW files from digital cameras often have a sidecar file accompanying them where metadata that's been added to the file is stored. That is the case, for example, if you've imported pictures from your flash card to FotoStation and added metadata to them there.
Other file types that don't support embedded XMP will also be coupled by a sidecar file when a FotoWare or other XMP-compliant application adds metadata to it.
To upload these files and preserve their metadata, you need to use the FotoWeb Desktop Upload utility. This utility will correctly identify the sidecar files and upload them in the same request.
You cannot use the Upload feature in the FotoWeb web interface to upload files that have accompanying sidecars, as only the master files will be uploaded and you will lose any metadata added to them.