I have a monster server, 12 cores, 76GB of RAM, solid state raid array, etc and when I first bought it, I chose windows server 2008 64bit as the OS. The computations I perform are pretty intense and run for about 24 hours utilizing about 22 threads. I have spent a lot of time performance tuning this code, so I was familiar with the overall performance on the previous server I was using, which ran Windows server 2003 64bit.
Anyway... My .NET 2.0 c# code ran significantly slower on 2008 versus 2003. I narrowed the problem down to I/O system calls, then lost interest and backed down to Server 2003. The newer windows code just did not deal with huge I/O operations as efficiently. I tend to snarf a couple of terrabytes of data a day...
You might try upgrading RAM. Make sure you have all the service packs. I'm don't know if your macros will work 100% on the latest version of office. I had a bit of trouble with some of my VB Automation code once I moved to 0ffice 2010.
I feel your pain and ahve experienced basically the same thing. I want to upgrade OS's on my servers, but I'm stuck on 2003 until CPU's catch up with the performance degradation.