cpu lag

[gaeorn]

It is very difficult to diagnose a performance problem under linux with just one screenshot of top. There are simply too many factors. However, I can give you some pointers as to where to look.

Since this ran well on a prior server, I would look for any differences between the two systems. You said the new one is missing one CPU, but since in that screenshot you are showing 45% idle time, that is less likely to be the issue. Have you looked at the performance numbers for the hard disk to see if it differs significantly from the old system? Is MySQL configured exactly the same with all the same table types, etc., as the old system?

Just look for anything that is different, no matter how slight a change. One (or more) of those changes should be the cause.