I recently had surprises washing ABC negs with gentle agitation, resulting in low stain, I thought it could be same thing, washing directly in Jobo being much more violent (I washed during 30' as usual in trays, maybe a bit long for a Jobo ?).
I never wash the negatives in the drum. After the rinse in hypo-clear, or in my case a 1% sodium sulfite solution, I place the negatives in a tray for wahsing for 20-30 minutes. As far a I can tell there is no increase in stain during washing, and if so, it is very minimal.