The only way to understand what is going on is to check the log files for these vizql sessions. From the begin-end pairs you should be able to check what vizql command takes more time and follow that path to drill down to the cause of issue. Was the render that took more time? Or the data access?
Good news, that Tableau is working on a feature that will help a lot with performance issue detection and will eliminate the need to measure cpu utilization from an external process. This feature will be most probably shipped end of this year and will be a game changer for admins looking for workbook performance issues.
Tamas - that's encouraging news to hear!