It is normal to see a difference between the CPU usage reported in ControlUp and the values shown in Windows Task Manager. This is because Task Manager calculates CPU usage using different and undocumented methods depending on the tab you are viewing. At least some of these values are likely to be different from ControlUp’s reporting.
Microsoft has acknowledged these inconsistencies and announced plans in the Windows Insider Blog to update how Task Manager calculates CPU usage.
The ControlUp for Desktops Agent calculates CPU usage using the % Processor Time (Instance=_Total) counter from Windows Performance Monitor (PerfMon). The Agent samples this metric every 3 seconds, and the value you see in ControlUp is the average of the last 20 samples (1 minute of data).