I'm assuming you are doing weighted barbell squats?
Whenever you come back to doing an exercise after a long period of time the DOMS (delayed onset muscle soreness) that you feel will last longer.
However based on your routine I would say that you are probably squatting far too often, for a big exercise like squats, I would give yourself at least 48 hours rest in between squat sessions.
If you are constantly overtraining your muscles, they will never have time to recover properly and will not rebuild or grow to their full potential, in fact you may actually be negatively impacting your muscles by overworking them.
You will see much better gains if you limit your sets to 4 or 5 in a session, using a weight that you can handle with proper form, but still causes you to work hard. Follow this up with a 48 hour rest gap where you do no squats or heavy resistance leg training.
e.g. Squat monday at 12. p.m, rest 48 hours, squat wednesday at 12p.m, you will see much better results in the long run.
Let me know if you have anymore questions or if I have misunderstood you.