I am using Quicken 2007 Premier, but I had this same problem with Quicken 2006 Deluxe.
When I download from Vanguard, Quicken wants to create duplicate place holder entries, adding, and removing the same mutual funds with identical names. For example:
Pacific Capital Small Cap Y - Shares in Quicken - 0, shares in Vanguard
123.456 Pacific Capital Small Cap Y - Shares in Quicken - 123.456, shares in Vanguard - 0.
Any idea how to fix this, or why it is trying to add and remove identical entries?