@User:  I forget where the thread was, but you claimed that you could swap + and - pins of an op amp and it would pass LVS. . .  Yes, you are right.  This basic pin check was in the netgen code, but a routine was added before it that is supposed to just match all pins by name for black box entries.  Problem was, it didn't actually check if the cell was a black box or not.  That caused netgen to just quietly ignore pin mismatches as long as the names were the same (working on a fix now).