Scirocco Central

Hi guys,
It's been a while!! Anyway, I don't drive my 'rocco much anymore sadly as I've decided to just walk everywhere during the week.
I had it parked up for three weeks and decided to go for a drive last week. For the first 2 miles, there was a knocking sound coming from the rear nearside wheel every time I braked. It soon disappeared after a while... does anyone know what this could have been?

It's probably the surface rust being scrubbed off the discs because the car has been sitting for a period

Ah ok, was just hoping the brakes weren't damaged! Thanks for the answer bob.