I have noticed since Agent upgrade from version 2 to 3 CPU graph total is not 100%.
Screenshot of this problem attached.
Zabbix Agent was upgraded to version 3 on 02-03-2015, you can see the difference on the graph.
Another user confirmed this problem on a forum post :
(another screenshot attached).
The idle CPU time value repoted by agent may be wrong ?
The value reported by agent seems lower than the value reported by 'top' command.
ZBX-10710 system.cpu.util show incorrect utilization