The issue was present in the cable between the small adapter board and the rear panel. The cable and the Dsub 25 connectors were replaced. The removed parts were resoldered. Did the basic test of the channel.
Attachment 1: I cleaned up the area of the PD3 circuit of S2100556 and checked the voltage when the circuit was energized. The PD photocurrent line from the rear panel had S2100556 even with R25 removed. So the problem was between the rear panel to the outer side of R25. I've started to remove the cables to localize the issue and found that the issue disappeared when the ribbon cable was removed.
Attachment 2: I didn't investigate how the ribbon cable was bad. It was just trashed. The cable and the 25pin Dsub connectors were replaced and the line in question looked normal.
Attachment 3: All the components removed were stuffed again. The I/V-output of the circuit showed a 0.7mV offset but it seemed within the normal range. By touching R25 with a finger made it up to ~10mV as the other channels do. BTW: For 1000pF cap (C10) I used a stock 1000pF cap (KEMET, C330C102JDG5TA, 5%, 1kV, C0G) instead of nominal one (KEMET, C317C102G1G5TA, 2%, 100V, C0G).
Attachment 4: Noticed that the jumpers for shield grounding were missing. So they were installed (Attachment 5). This jumper is connected to Pin13. This line becomes Pin1 of the Dsub25 sat-amp cable because of the adapter board D2100148. The sat amp cable is D2100675. Hmm. In fact, this line does not touch the shield anywhere (unlike the aLIGO case). So only the chassis provides the cable shielding, no matter how the jumpers are connected or not connected.
Attachment 6: Final state of the circuit