I've heard of people developing all sorts of issues with green coffee and jute (allergy wise)
Richie wears a dust mask around the green coffee because it gives him hayfever symptoms and he also avoids contact with the chaff.
This is very interesting; I put up with hayfever every spring, but have had no problems with chaff so far (in home-roaster quantities). I don't know about jute.
However, there is an immunological reaction well described in cotton / fibre workers, byssinosis, which is of course pretty rare in the West now. It's a chronic hypersensitivity reaction, which happens in some people but not others.
There are a very few papers on pubmed, regarding jute and immune reactions.
Those I can find are of uncertain quality (eg only abstracts available, the rest not in english, small journals etc). The most recent concludes intriguingly; "Our data suggest that immunological reactions are not likely to be responsible for the development of respiratory impairment in textile workers exposed to jute and sisal dust."
This suggests that respiratory symptoms when exposed to fibres (eg jute, sisal, ?cotton) may be distinct from allergic-type symptoms.
Steve (L), if you find you react to some jute sacks, but not all, perhaps there is something else on the material of the problem sacks? If those indonesian sacks were damp at any point, they could have bacterial endotoxins on them - and these could be your allergens.
As for chaff - I've even less idea. If greens are fine but chaff is a problem, it's unlikely a toxin is to blame - that would have been lost during the roast.
I don't think I can be much more of a help - there's not much research in this...