High disk activity on SBS 2008 and SBS 2011 is an ongoing concern for our clients. Just yesterday, we had an SBS 2011 server with so much disk activity that it slowed down the Hyper-V host so that all VMs were not performing properly.
To diagnose this issue, use Resource Monitor to view the Queue Length. When there is a problem the Queue length for a drive will be high and sustained. The % Active Time will also be high. These indicate that the disk is busy and has a backlog of work to perform.
It's important to note that the actual disk I/O may not be that high. In our case, the Disk I/O was less than 10 MBps which is far less than the disk system is capable of. The Disk I/O can be low but the disks busy when many small operations are performed.
The fix for this is almost always recreating the SBS Monitoring database. The SBS Monitoring database grows over time and eventually becomes a performance issue. We don't use any historical information in that database. So, removing it and recreating it is a good solution for us. It's a 10 minute fix that lasts for about a year before needing to be done again.
Microsoft instructions for how to recreate the SBS Monitoring database are here:
On a physical host, the SBS Monitoring database will cause high Disk I/O on the C: drive. On a hyper-V host, the SBS Monitoring database will cause high Disk I/O on the physical drive that is hosting the C: drive VHD for SBS. Monitoring Disk I/O inside of a virtual machine will not be accurate.