First of all, do you have any video of you using the rubber guard? That might help to troubleshoot it. Also, who did you learn it from? Is it somebody who read it in MTRG, or have you trained with somebody who has trained with Eddie or has a lot of experience with it? There are a lot of little details I've learned about rubber guard that aren't in the book. It didn't work as well for me until I spent some time with Einstein and Eddie.
If I start in Mission Control then I almost never hang out there with the foot on the hip because I find it's a higher risk of getting passed. I transition immediately to Crackhead, or at least drape my other leg across their back, so I am generally in Crackhead a few times each rolling session.

Of course, I rarely hang out in Crackhead, either, unless I am tired and need a rest; I'm immediately working either to get their elbow to the centre of my body for an armbar or a sweep, or their hand to the mat so I can clear the neck and work from there. I find that Crackhead helps prevent the stack because it makes me so heavy on them, and they know something is coming, so they're more focused on keeping their elbows tight.
Sometimes it's best to just give it up and try for a sweep. How's your squeeze? Is it tight and sustained? That makes a big difference. If I can get them tight to me and they try to stack me, it puts their weight higher towards the ceiling, and they're already pretty low in my guard, so I have a lot of space and leverage to sweep them. I squeeze as hard as I can, tuck my butt under them and roll over my shoulder, driving their face to the mat, and ending up on top. It's not pretty, and it's something I just figured out on my own, but it sometimes works for me.
I've never had any back problems with Rubber Guard, and I use it a lot, but I am also freaky flexible and quite strong for a girl my size. One thing I would suggest is, before using it live, you spend a lot of time drilling the positions and techniques. Not everybody's body can handle rubber guard on day 1, no matter what people say. It's fun to do, it looks cool, and it's very effective if you understand it and have some experience with it, but it requires very specific traits and strengths that you should work on before busting it out in rolling or competition.