Thanks for your comments Sekerob.

He does run as administrator, and he is a system administrator, so his Task Manager is showing the BOINC CPU usage. We've noticed also that if BOINC is set to 10% CPU usage then the Task Manager shows regular spikes of CPU activity, this jumps more on other levels. He has a dual core laptop. His peripheral vision is tuned in to seeing the Task Manager and he dislikes that constant jumping, and yet he wants to see the Task Manager since he likes to monitor his CPU usage. Hence my original quest to find a way to tell Task Manager to ignore processes that run at idle priority.

We have come up with another scenario that hopefully is going to work well. We've turned off the 'Computing allowed while computer is in use" and set the "Only affter computer has been idle for 1 minute" setting, and bumped the CPU usage to 100%.

Hopefully this will give us greater processing than the 10% level, which with his usage per day and his laptop sometimes being on batteries was causing units to be completed outside of their 10 days of alloted time.

All the best,
Cheers,
Mark

A little bit hands on is the 3rd party ThreadMasterGUI control application. Offers very smooth throttling from W2K through W7 and server versions and only needs a tweak when a new science comes out or the version is updated. See Start Here FAQs for more on this.

Perhaps just use one core and set Boinc to run after 1min of non-use.
This is the same as running 2 tasks at 50% with the exception that only 1 task will run at a time, so it will finish faster / or have more chance of finishing in time! You should note that tasks do not all save at the time the computer is shutdown and therefore restarting tasks at the last checkpoint can lose a few percent of completed work. Some of the FightAids@home tasks are doing this with me.
If you are trying to run 2 cores at 10% or even 20% it is unlikely that you will finish many tasks.