Do you think you would have an idea or a suggestion on the next thing to look upon?
I saw that our server have proxy installed but not enable. Would it help to enable it? I already have imapproxy installed on another server though.
Thanks in advance!
No, I don't think the IMAP proxy will help. In a single-server setup it'll just add another process in the middle.
I'm not really sure what the next step would be. What type of CPU is in this box? If you run top while this thing is crawling, it should give you an idea of what the CPU is doing (i.e. % in user, % in sys, % in wait). That would be good to know.
Also, you said I/O stays at a constant 1Mbps, does it grow with the CPU trend during the busy times? Most of the time, these MySQL slow queries are caused by I/O problems either directly (slow RAID) or indirectly (not enough memory, causing more I/O). On that note, what kind of a disk system are you running (RAID type, disk type, DAS/SAN/other)?