Ok, re-reading carefully and checking the referenced thread, I finally understand this in detail. It's not that bitcoin "empties your wallet" at each transaction - it fully empties an address used to send coins. In this particular case, the user had previously sent themselves the 9000 coins in a lump, resulting in all those coins being held at a single address.

So far as I can tell, there is no way from the GUI client to actually get at the information of what coins in your balance are held at what addresses? Given that the addresses are what is "really important" that information might be of value.