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
HP - http://h20000.www2.hp.com/bizsupport/TechSupport/Document.jsp?lang=en&cc=us&taskId=110&prodSeriesId=428936&prodTypeId=15351&objectID=c01075682
Citrix - http://support.citrix.com/article/CTX114782
IBM - http://www-01.ibm.com/support/docview.wss?rs=0&q1=opteron&q2=usepmtimer&uid=swg21267793&loc=en_US&cs=utf-8&cc=us&lang=en and ftp://ftp.software.ibm.com/systems/support/system_x/41y7884.rtf
Hope this helps in your travels.