Weird. To be perfectly honest, it seems unnecessary and a waste of buttons to have undo set to two. Pick one. It might be your having it set to two that's causing problems in the first place. Hell, I use a Companion 2 and it comes with two buttons on the pen, an eraser end, six buttons on the tablet, and a radial menu. It's still not enough sometimes lol but the Create doesn't have near as many. Pick one, experiment with which one you like more (honestly having it on the pen would be better for the desk tablet that you're using - I use it on my button settings because my tablet's portable and I'm always holding it, unless I've got it off to the side and I have a keyboard, in which case, CTRL + Z. However, there is a higher chance of you accidentally hitting it and double clicking because it's on the side of your pen.)
Are you sure you're not just accidentally double clicking it? You might just be putting too much "click" into your clicking. Check your pen settings too, make sure it's not set to default double click.
Other than that though, again, seems a little unnecessary to have undo set to two buttons. Maybe a button for undo AND redo, but whichever one you use more/works better for your work habit, pick one and go with that lol 