I have the exclude working fine, and in this case that is probably what I wanted anyway as the files have already had their integrity checked at the original location and I do not intend to delete the original files.
I thought it was worth mentioning, though, as it is quite possible that you do not want the plugin to check a hard link (assuming it can detect them in the first place). Having said that I am surprised that an error is actually reported. I would have expected the extended attribute information to either be present on the hard link entry as well (in which case why the mismatch) or the plugin would generate a new set of extended attribute information. I will have to look at this information on my system to see if I can sport what is generating the mismatch information.