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5:10pm
Omar found that one of the LV mezzanine card (L5t, bottom screw) was now connecting AGND to the FEB support plate. The screw is touching the ground plane. By pushing it slightly he was able to get it back in w/o touching. 

5:30pm
L4t and L4b power was swapped on the back of the breakout box (on the flange side). For reference this is patch panel P3 and thus S1 and S2 where swapped. Mapping power to FEBs is ok now.