The cable cover does not mess with the flex of the boot...people just want a excuse for their shinbang. However, it does make the cables go in a weird position if you're not careful (sometimes the cables get too close together and end up and the same groove in the tongue...if you want to keep the cover on you need to be careful to make sure the cable always goes in the proper place). What's giving you shinbang is backseat landings and skiing, you need to make sure to always ski and land with your knees inline over your toes. The main reason I see this most commonly is from trying to afterbang by just leaning back, this cause a ton of stress on your shins and causes shinbang. When you land, if you want to afterbang you still need to keep your shins against the front of your boot and your knees over your toes. Also, when just skiing around, just make sure to stay in a "natural skiing stance"...i.e. knees over toes, weight forward, ect.
I've noticed a lot of kids lately that either never learned how to ski properly and just went for trying to look good in the park, or just completely forgot how to ski while they're learning park...and then complain about shinbang or snow conditions (I'm not kidding...I've had kids ask for the park to be groomed on a 20" powder in CT...something we never get). So this is kinda a sore subject for me, so sorry if I sound like a dick, I by no means am accusing you of not knowing how to ski...I'm simply explaining the #1 most common way to get shinbang.