Record-low interest rates are a boon for home buyers and for homeowners seeking to refinance. But low appraisals are making it difficult or even impossible for some borrowers to take advantage.

Samara Glassman and her husband, David, knew their ranch house in Phoenix had fallen in value. But they were surprised by a September 2011 appraisal valuing the four-bedroom home at $385,000, down from the $604,000 they paid in 2008. The appraisal put the couple underwater on their $402,000 mortgage – and threatened to sink their plans to refinance.

When they examined the appraisal, they saw it was based on older homes a few blocks away that weren't directly comparable, says Ms. Glassman, a real-estate agent. They got a second appraisal in January that placed a $500,000 value on the property.