I'd say it is due to the major downturn we had in hiring (and population) post the dot-com implosion.
the chart below compares seattle's job growth vs. national growth (left axis and solid lines), and home appreciation vs. the Case-Shiller 10-city index (right axis and dotted lines) for the period of 1990-2007.
What you will see is that Seattle housing is appreciating faster than the rest of the country up until about 2000, then the job losses start and the lines cross. We then fall behind the other markets until just about now... So we were behind - but we've caught up.
Note that I used the 10-city index because the 20 city index only goes back to 2000.
D