John,
I was not back to this forum often.
Here is the update.
We upgraded to 64-bit Windows server 2003 Enterprise edition on all DEV, Test and production environments couple of months back.
Also, the version of BI server is 64-bit.
So far, everything is working great. Transformer also doesn't have any issues.
From our experience, 64-bit on 64-bit OS didn't cause any issues.