So for your SMT1/SMT2/PTH boards, you have poor solderability during SMT2. [Even if you have no SMT2 and only ST1/PTH, our answer is the same.] We assume this occurs on one board part number only.
We guess that your bare boards have insufficient gold to provide adequate solderability protection of the second side. Gold thickness below 3 thou is porous and would allow corrosion of the second side nickel during first side reflow. Verify this theory by making sections of the bare board and measuring the gold thickness.
I think the oxidation on the pad happens easily but do not on Au plated pad.The reason may be caused by improper cleaning or Au plating thickness in plating process. But,before suspecting the pcb board, you need to check your process or used material first to verify the variation or improper. Thanks