Win 2003 X64 + SQL 2005 &< Win 2003 32 + SQL 2000?

I may not be the best forum for this post, however I believe some one
can still help me or direct me somewhere else.
I'm finding that win 2003 x64 and SQL 2005 CTP is slower than win 2003
and SQL 2000.
Machine A: Opteron 2.2 (248) w/ 2 cpus. 8GB memory. SCSI disk array.
Windows Enterprise 2003 x64 final release. SQL Server 2005 enterprise
CTP.

Machine B: Opeteron 2.2 (248) w/ 2 CPUs. 4GB Memory. IDE Drives.
Windows Server 2003 (32bit) and SQL Server 2005 (standard).

I'm using Cognos' DecisionStream as the ETL tool (32bit). I have the
identical job on both machines. Machine A is slower to do my nightly
build (1h 20m) vs. Machine B (50m).
I've done no tweaking of the databases. I Used SQL 2005's studio to
copy the database from Machine B to Machine A.
The only major difference is the O/S and SQL, the machines are same
speed, however Machine A has twice the memory and faster disk; so I
would expect it to be faster.
Can anyone think of smoking guns I might be missing?
TIA