LabVIEW uses URL format for its XML based paths which happens to be always Unix style. Symbolic paths are rather something like "<instrlib>/aardvark/aardvark.llb/Aardvark GPIO Set.vi", however the HTML expansion does make that a little less obvious in Dan's post.
To my knowledge LabVIEW only should use absolute paths as reference if they happen to refer to a different volume. On real Unix systems this is of course not an issue as there you have one unique filesystem root, but I have a hunch your colleague may have accessed the VIs through a mounted drive letter. I could see that causing possible problems if the VI library was loaded through a different drive letter than the actual VI. Shouldn't usually be possible but its not entirely impossible. The actual path in the XML file may not show to be different because the path handling that determines if paths are on the same volume works likely on a different level and when the paths are finally converted to the URL style format they are most likely normalized, which means reducing the path to its minimal form and that could resolve drive aliases.