Hi,
Sorry I can't help with the "control window" thing, but I'm sure someone else will be along very shortly to help with that one.
As for the Java zip's, I'd say you can almost certainly not worry about them. There's been quite a few threads on that topic, as you may have seen, and to this day I'm not sure anyone's come up with an explanation. (At least that's the way it seems.) But "corrupted" zips in Java folders during a scan seem to be almost universal among us -- if your Java seems to work fine, don't lose any sleep over them.
Oh, and I think I remember they'll scan just fine if you do them individually with the Explorer shell. Right-click on each file in turn and select Scan.
Best,
Mike