As with many things, prices are local--very local. In addition, price indices are rarely apples-to-apples comparisons. They usually take prices on one date and compare them to prices as a whole on another date. For example, the Case-Shiller Index actually takes the total sales of all the property in a city and compares it to the total value of the property sold in that city in an earlier period, to calculate the rise or fall of real estate values over a period of time. That means that it's hard to know what would happen to one specific property when it got sold or resold.
In the current market, sales are being driven by first-time homebuyers and are strongest at the low end of the price spectrum. Overall, prices are flat or still falling slightly, although this does lag in time, due to reporting delays. However, we are beginning to see appraisal problems again, which had not been occurring in recent months. That indicates that prices are rising, thereby pushing up sales prices above levels of past reported sales, which are used by appraisers to calculate value.
What's the bottom line? Prices at the lower end are being squeezed by supply and demand factors, and are probably heading up. Higher-end sales are still waiting for that phenomenon to take place.