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This indicator points to falling home prices

Daniel Acker | Bloomberg | Getty Images

While the headlines suggest that home prices continue to rise but at a slower rate, the reality may be different, at least according to one measure.

A housing index compiled by Allan Weiss, who co-founded the widely followed Case-Shiller Index, looks at individual home sales across the country and actually shows price declines in the major markets.

Writing in HousingWire, analyst Chris Whalen believes indexes like Case-Shiller don't tell the whole story. Whereas that index focuses on 5,000 averages in certain zip codes, Weiss' measure looks at 50 million actual home prices.

Through the end of March 2014, the data from Weiss shows that home prices for 1,000 square foot single family homes have fallen—1.1 percent in Chicago to -2.4 percent in New York. Relatively hot markets such as San Diego, Miami and Los Angeles were also down, albeit to a lesser degree, while Phoenix was unchanged.

Whalen asserts that the post-recession period of home price growth came largely from factors that have dissipated.

Read MoreHousing a 'crappy investment': 'Mr. Wonderful' O'Leary

The housing boom of the 2011-2013 period was not a normal example of home price recovery, but rather a spasmodic reaction to the process of working through millions of foreclosed homes in the wake of the subprime bust. The fact that home prices were rising 5-6x GDP growth suggests that the upswing was unsustainable.

Read the full analysis here.

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