Why is taking a break more sore than when I run?

I have been a high milage runner for the past two years. I had an operation that made me take a month off in July and from August I have consistently been running maybe ~60-90 miles a week. I have tried to take rest days at least once a week (or at least cross trained or did yoga). For a number of reasons I decided I needed to let my body rest for a longer period of time and since Wednesday I have not run/cross trained (only done some light yoga).

Throughout my running I rarely feel sore or stiff or injured. Yet the last 4 days have been agony, all my joints hurt, my muscles hurt - especially my ankles, knees and hip joints. I don't really understand why this is the case?

Any ideas?