If you feel you can't get your checks in time due to your stance maybe being too forward heavy and wide, distribute your weight 50-50 instead of 80-20 forward
You'd also look at your opponent's chest to see movement, and time/predict based on it. Its MMA so dutch combinations are fairly common, expect a leg (or any kick) to come after 2-3 punches.
You'll also find you'll use multiple stances in sparring/fighting, not just one, and it will also be determined based on your opponent as well. If you face a wrestling takedown machine, you'll want to have it more front-heavy; Compared to a guy with a long history of a striking background where you'll keep the stance a bit more 50-50 or traditional Thai, or your leg will get destroyed.
Work on it with shadow boxing, you probably already know this, but SB its not just for offense, you need to work your defense, and footwork in SB as well. I'd even say its more important for the latter.
Do alot of partner drills for checking, this is something pad and bagwork can't really address as well.
Another reason is that you're probably not used to it, when I first started sparring and camp, after eating about 5 leg kicks in sparring, I was out for a week and walking was extremely difficult. My sparring had to be boxing-based since my leg was gone, and even then it was a bitch to do. These days its fine, after a hard sparring session where I eat about 3-5, I'm fine the next day.
Cheers