Here's my two cents (and I could be completely wrong, but I'll try anyway!!!)
One of the things you're trying to achieve when doing muscle work is the muscle "fatigue". So, when it starts to hurt, that's when you're doing the real work--obviously, you don't want to get to the point where you're screaming in pain, but it's definitely going to be uncomfortable!!
At muscle fatige (I learned this in my anatomy class), you're getting microscopic muscle tears and recruiting muscle fibers. This is what makes you gain lean muscle mass.
On the FLIP side, I've also read that as long as you get your work-out in (regardless of whether it's split up during the day), you're getting the same work. I don't know if I believe that, but...who knows?
So I guess what i"m trying to say is that I'm inclined to believe that you might be achieving muscle fatigue and doing more effective work if you do it all at once (ie, 80 squats in a row....OUCH!! vs two sets of 40...still OUCH, but less).
Take what I say with a grain of salt. I think it's wonderful that you get the workout in, period!! You should be proud