Artifacts copied with CopyArtifact seem to not record full paths in fingerprints. Only the filename is recorded. This could be fine – except the "See Fingerprints" page seems to only display one line for each file name. (That's probably a bug too.)
I would think that on the CopyArtifacts side, it should be quite a simple fix, in FingerprintingCopyMethod.java, which seems to be recording fingerprints with s.getName(). My quick guess is that the whole path could be stored if s.getName() was replaced with something like s.toString()...