After the whitening chassis was swapped, the worst problem went away, i.e.  QPDA seg2 looked healthy.  However, smaller problem, i.e. the dark noise level of QPDA seg4 being about a factor of 2 or 3 higher than everybody else (attached top), persisted.

Disconnecting QPD cable from the transimpedance box did not change the behavior, but disconnecting the cable between the transimpedance box and the whitening chassis did.

Anyway, QPD transimpedance amps was also swapped and everything looks good (bottom).