Hi ianb, and welcome to the avast family,
If you have reporting enabled and check the report after the scan, I'll bet you'll find that avast couldn't scan because of a "corrupted archive". What Sun Java (I presume that's what you're using) calls "zip" files aren't true zips, but use their own oddball compression method. And that seems to be the favorite target of the byte-verify thing.
I suspect that any infected files that are turning up are probably in your Java cache folders and nowhere else. Those are easy enough to get rid of, just open your Java control panel and empty the cache.
Hopefully that'll get you cleaned up again. If it's still turning up afterwards, let us know and someone else should be able to give you additional help.
Best,
Mike