Let me repeat something I wrote here last September:
The two indices have three principal differences:
OFHEO has only houses financed with conforming mortgages (those with balances of less than $417,000). CS uses all sales.
OFHEO includes appraised values for refinance loans. CS looks only at sales.
OFHEO includes houses that may have been substantially improved from one sale to the next. CS throws those houses out.
I think the last of these three points is especially important in partially explaining the difference between price indexes.