My son went through this same thing last season at 13u. I could see when he warmed up based on where his elbow was if he was going to have a good day or a rough day. Elbow low = bad day.
If you feel like you're throwing mechanics are segmented on the bad days, I bet it's a leg strength issue. The chain gets broken and the upper body struggles to catch up. If the legs (and hips) don't fully fire, the timing gets off, thus the feelings like the chain is broken into different parts that don't flow.
Focus on leg conditioning now, and make sure you get fully stretched and warmed up during the latter parts of the season when it gets warm. The tighter you are, the longer it takes for your legs to get loose. It's easy to forget that when the weather gets hot.