Any chance that the lingering flavor is a metabolism off-flavor? You could test it by boiling some of it in a pot to 240, letting it cool, then mixing water back in to get back to proper density - that technique will remove the nasties from the metabolism off-flavor (if it's worth the effort to do it for huge batches of syrup is another question entirely)
http://www.uvm.edu/~pmrc/off-flavor2.pdf is the doc that talks about eliminating metabolism off flavor. AFAIK it doesn't do anything for buddy flavor.