Ideally you meet an attack with the timing that put attacker hand, left and right shoulder on the same line or little behind the line of his shoulders. And then you are shifting you weight lightly forward. That happens in the first moment of the contact and should shape his backbone to the back. It means that the direction of unbalancing is to his third point behind his back. Continue to stretch his arm to this point while you are doing shihonage. You have to maintain not only the contact with his attacking arm, but stretch and lock this arm all the time during the turn of your hips. His arm must be stretched(you can put your elbow under his elbow) and in horizontal position while you pivoting. That maintains unbalancing.
I think this is most correct for what I think you are experiencing. I had the same issues with this technique, an as a result, never really considered it a viable technique for what I do.
My problem was, I would do really well at affecting uke's balance on the initial entry and blend, then essentially give him his balance back as I turned to pivot for the throw. It wasn't just ura but omote as well. I made it my sole mission in training to resolve this and come up with the following.
After I blend with the attack, I when I grab uke's striking hand, I grab the wrist along the line of an American Indian Handshake. That is I grab his wrist or forearm area closest to the wrist with my palm on the inside of the forearm or wrist. As I step around to pivot, I extend
both of my arms, similar to doing boken technique so my grabing hand is on top of my non-grabbing hand. My non grabbing hand acts as a sort of platform for uke's arm and prevents him from being able to turn into me and out of the technique. My grabbing hand extends out in front of my forehead and stays there throughout. If you allow this to collapse, uke regains his balance.
The important point being, is the way you grab uke's wrist or forearm. By grabbing with your palm on the inside of the forearm. when you extend your arms uke's arm has a twist to it which causes him to maintain that arched back posture as you pivot. Your extended non-grabbing arm gives him some support so he doesn't just try to twist out of the technique. As you pivot around it is essential you don't allow your extended arms to collapse at all. Maintain a constant extension. You may have to even sink down a little more to clear uke's arm. By the time you finish your pivot, uke should no longer be able to stand on his own. The small amount of support you are giving him is what is keeping him standing. As you pivot end by turning to face him. At this point you have a grip on his forearm similar to a boken grip. Move your center forward and cut down along uke's back across his center and he has no choice but to fall.
I know some people like to apply a wrist lock in shionage as they take uke down, but I learned it initially to grab the forearm not at the wrist or hand. I also like coming all the way around to a 90 degree angle to uke rather than being along side uke facing the opposite direction. This is how I do it, for now, hope this may help.