install sysstat package then run the following command from a terminal:
sar 15 3
exit all running applications, including net_applet and conky/gkrellm if any and repeat the above command.
switch to runlevel 3, thereby using text console, and run again the above command:
init 3
sar 15 3
the result should help to identify the context of the unusual high load, being the system, the GUI, or some apps ...