I think it is a normal part of having a newborn, like others said. Biology gives you that time when you live in a little bubble with the baby and nothing else seems to matter quite as much. It helped me to have some specific activities to do with my step-daughter while my husband took care of the baby. It also helped to talk to my husband about taking over most of the "big kid" stuff for the first 6 weeks or so.
I also think there are SO many times in being a step-mom that we second-guess ourselves, especially when it comes to worrying that we feel differently about our bio vs step kids, or worrying that we treat them differently. I have 4 kids, 3 of them biological and 1 a step-daughter. I can say for certain that I treat all of them differently and I don't feel the same way about all them. That's not to say I don't love them all totally and completely, but I have a special bond with each of them because they are each their own person and we have different relationships. There are things about each of my kids that I love and things about all of them that drive me a little nuts. But I don't spend nearly as much time worrying that there is some deeper awfulness about my biological daughter driving me nuts as I do about seeing my step-daughter's crazy-making quirks.
I think with our own biological kids who live with us full-time, there is this sense that I know 100% of their life and personality, and with my step-daughter there is this whole part of their life that I don't know and can't see, and we're sort of in the dark about how that part of her life may be influencing her. I can "read" her as well as I can read the other kids, but it's like looking at a puzzle with some of the pieces missing... so it's always a little harder work and a little less comfortable... I always feel like I'm working with less information than I need to do the best job I can.
So, give yourself a little bit of a break. The fact that you are worried about it is a good sign, and a good starting place to try to find some ways to address it. Step-mothering is the hardest thing I've ever done and most of us are making it up as we go. I usually figure that, even at my worst, I'm doing better than a lot of people might in the same situation.