The Fannie-Freddie system -- known as the Home Valuation Code of Conduct -- is complicated by the fact that it is a byproduct of a legal settlement in 2008 between New York Attorney General Andrew M. Cuomo and the two government-sponsored mortgage investors.

Under the code, appraisers are now routinely assigned by appraisal management companies rather than being selected by local mortgage companies or loan officers. The management companies pocket as much as 40 percent to 50 percent of the appraisal fee paid by the consumer.

Frustration with the new system boiled over and made its way to Capitol Hill late last month. The National Association of Home Builders called for an immediate change in the rules governing the use of foreclosures, short sales and other distress transactions as comparables for appraisals on non-distressed, typical homes, whether new or resale.

Two congressmen -- Travis W. Childers, D-Miss., and Gary G. Miller, R-Calif. -- have introduced legislation calling for an 18-month moratorium on the appraisal code. In identical letters to James B. Lockhart, the top regulator of Fannie Mae and Freddie Mac, and Cuomo, the National Association of Realtors also requested a moratorium and complained that the code is raising consumers' costs, distorting property values and killing sales.

Asked for comment, Lockhart said through a spokesperson that his agency is "monitoring" the situation, and considers "the views of market participants important."

Bottom line: Be aware of the issue. It affects your equity, even if you're not currently buying or selling. And watch whether Congress fixes the problem.