What parameters is spamd started with? In particular, is spamd started with -u? If so, spamc's -u will be ignored.
I was - yes. But removing it and restarting spamd, and then rerunning the test doesn't seem to make any difference. It still isn't applying the bayes scores to that message even with:
spamc -u nick < spam3.txt :( Very confused now.