If during your troubleshooting, you run in to some counters (Disk Read/Writes) that just don't seem correct based on the way the server is performing, then you might be running in to a drift calculation bug with certain AMD processors. You may also see negative PING response times as well.
Here is what it looks like in Performance Monitor as a steady rise in disk response times.
Avg. Disk sec/Read Counter
Avg. Disk sec/Write Counter
Over time, this may look like a problem, but it really isn't, it is just that it is being reported incorrectly.
Clint Huffman, which is the creator of the PAL tool has a nice write-up on this problem at http://blogs.technet.com/clint_huffman/archive/2008/03/21/warning-perf-counter-data-might-be-inaccurate-on-some-amd-processor-computers.aspx
Hope this helps in your travels.