Maybe I have been reading Task Manager wrong all these years...
I thought this meant System Idle is NOT using resources - it is showing what is left over...in your case 95%+. The idle process takes place when the processor isn't being sent any other work to do.
I always thought that System Idle should be a high number - I do not know how better to explain it - it is totally normal for system idle to be high so system idle at 99% says the system is 99% idle.
Right now mine says System Idle 98 and is using 16K of memory. I just checked mail with Mailwasher and System Idle went down during this time to 94, once mail checking was complete it went back up to 99.
Computer is speeding along as normal.

Ignoring system idle, what else is using the cpu on the machine? Hard drive activity can mean something entirely different than processor activity.