Did you download the quotes with Download Quotes, or Download Historical Prices?
Download Quotes will overwrite all prices, but only for today and four (or so?) days back.
If there is bad data older than five days, Download Quotes won't do it. It's necessary to use Download Historical Prices. And on my Q'06 it would not overwrite the existing data - I had to delete them first.
Does anyone else see it that way, or am I fuddled?