Probably one of a couple factors:
1. your shoulder strength
2. The degree of incline of your bench. I've seen some cats doing incline where it basically becomes a military press
3. your technique. sometimes guys end up pushing mainly with their shoulder joints instead of focusing on pushing from...
I live off campus so I can just make all my food and I end up bringing meals to campus. It's sounding like you live dorms? In that case, you'll probably need to make sure you get the bulk of your calories during cafeteria hours and invest in snacks for other times throughout the day
Up your Mass by MHP is a solid gainer, carbs come from barley and oats.
I think we need to realize that, even though mass gainers are not ideal, they are not terrible either, especially if you are busy and it fits your macros. In all reality, where else are you gonna find a 50g protein, 80g...
In my experience, knee pain usually stems from inflexibility or misalignment of the hips. Get on your stretching steez, massage your hamstrings and hips, and maybe look into a chiropractor. It could also have to do with your arches, shoes or other foot related issues