I had no issues at all with my X-52 (Non-Pro) prior to installing their software. I installed it, then had to make a profile that disabled the shift functionality of the pinkie button in order to get it to function properly.
What you're mentioning here doesn't match my experience. I have all buttons mapped. The wheel does scan range, with the wheel click being my FA Off button. I have the "mode" buttons mapped to various functions, and the small click button by the mouse stick is also mapped. All of that basically stating that the full gamut of buttons CAN be mapped. (This said, I have intermittent issues where the wheel, while recognized in ED, doesn't actually work for changing my sensor range, so I have to resort to the imprecise thumb slider.)
I'm assuming (Ya ya...I know what they say about assuming) that you've gone in and remapped the controls in ED? Did you change what controller mapping you're using in ED? (I set mine to X-52 first, then went and custom mapped some of the buttons).