This is totally an anecdote, and I have no good explanation for why this occurs. However, I can tell you what I've done to solve it.
In my experience it occurs before fixing. I have done a test print, stopped it and then turned on the room lights in the darkroom to confirm this. Any tray or bottle can be contaminated, though, so where the problem occurs may just be a result of your darkroom process.
I strongly suspect that in my case, I have an unholy combination of fixer and indicator stop bath working its way back into the developer. In my experience, the print has a mild oder of sulfur and ammonia.
I have experienced this in my drum processor, too. I think it occurs when the drum has not been properly cleaned on a previous printing session. I have replaced all chemicals and doubled rinsing time to no avail. When the drum is the culprit, the only solution has been to scrub the drum and the reservoirs. Note, I use a Unicolor system, not a Jobo system; I'm not entirely sure how a Jobo system works so you may need to do some additional cleaning.
It would be nice if I could say that this has caused me to improve my darkroom cleaning habits, but that would make me a liar
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Jason