I am not saying this si your problem with site mail.

My site mail did not work after the change over. I was using Windows XP Professional 64 (because I had all of my pipeline setup there and did not want to rebuild.)  I worked with the Rendo IT department and learned that IE 8 was not fully supported. (Java was breaking). 

I had built a second machine for production, (Dual Xeon Windows 7 box).  I tried mail with that and it worked fine. SO, I am migrating all of my applications to the new machine.  IT was over due.