Brown water usually comes from the incoming water main - especially if the underground pipes are steel rather than the newer plastic. However, you'll find that your loft header tank has a fair bit of sediment in it and to clean it out it really needs to be disconnected and washed out with a hose pipe.
There is also a fair chance that the copper cylinder has also sediment in it, but there's a lot more work involved to disconnect that.....I get this fairly frequently and it hasn't done me any harmmmmmmm (!) and I just put up with it. The pump doesn't need to run all of the time (but it may have a hot water run down period) and I'd suggest it isn't wired up correctly.
John
January 2008