IMPORTANT DISCLAIMER: This answer merely presents a hypothesis, one that is difficult enough to prove when dealing with a child regularly and one that definitely cannot be proved given the amount of information provided here.
I see a possible answer in the attachment theory here, in particular in the child's attachment to its mother which is forming during the child's first year. The theory names several attachment patterns with the secure attachment being the ideal one - a secure child has confidence in its mother. So while this child also suffers from separation anxiety, it has no doubts that its mother will return.
What you describe could be a sign of anxious-ambivalent attachment however. Here the child didn't get a consistent response when it needed its mother's help, so its stress level when separated from the mother is very high - it doesn't know whether the mother will come back. In this case, your step son's reaction really isn't about anything that you do. Daycare is a similar situation, maybe you can learn whether the same behavioral pattern shows up there as well.
While for children this plays out entirely in the subconsciousness, this condition persists into the adult age. From such adults I know what it feels like: no matter what happens, you feel like you aren't worth being loved. So people doing good to you cannot be interpreted as an act of love, you rather expect them to act out of hidden self-interest. Consequently, you cannot possibly rely on other people, everybody is a potential threat.
Some people are spending years fighting their subconsciousness in order to improve this attitude. So unfortunately I can offer you very little advise should this hypothesis turn out correct. Then again, this child is closer to the source of his issues so fixing them might be easier - you will definitely need professional advise however. Also, I'm fairly certain that nothing will work without the child's mother being cooperative. I can imagine convincing her that her child needs help being pretty impossible.
But I hope that you will at least manage to understand what this child has to put up with, and why he is resistant when you try to comfort him. As he grows older he should develop better ways of coping, and maybe you can find a way to assist him here.