True, but there are caveats.
During the 104th Congress (1995-1997), 105th Congress (1997-1999) and 106th Congress (1999-2001), the Republicans were the majority party.
In the 107th Congress (2001-2003), the Senate was equally divided between the parties, but the Democrats held the majority due to the deciding vote cast by the outgoing Al Gore.
But, the Republicans became the majority party again in the 108th Congress (2003-2005) and held it through the 109th Congress (2005-2007).
The House was been under the control of the Republicans from the 104th Congress (1995-1997) through the 109th Congress (2005-2007).
As you point out, during the years Bush was supposedly trying to reform Fannie and Freddie, the Republicans controlled the government.
So, if there was malfeasence in the government it was because the Republicans let it happen or were active participants.
Until the conservatives admit that a good portion of the GOP is part of the problem it will never get fixed.