Diagnosing high CPU waiting
Solution 1:
i/o wait is also generated by NFS, SMB and other remote filesystems.
Use vmstat 2 to see a granular view of system performance including io wait.
Solution 2:
High wa generally does mean the OS is either waiting for network or disk. There is quite a nifty program called iotop. This tells you what the disk is up to, might be some help.