It really could be any number of things contributing to such a performance difference.
Poor graphics drivers can cause simple graphics calls to take exorbitant (by the cpu's standards at least) amounts of time. Try reinstalling them to the latest and re-test.
Virus scanners can cause apps with heavy file I/O traffic to slow down immensely. Try disabling any virus scanners and re-test.
Disk fragmentation can cause performance problems (but typically not trigger lots more CPU activity) when opening large files, such as huge CAD drawings. You could try to defragment your drives and re-test.
Heck, even something as zany as a poorly cooled (or uncooled) CPU can trigger the P4's thermal protection circuitry to kick in periodically, slowing things to a halt. As long as the CPU's fan is running, this shouldn't be an issue.
To really diagnose the problem, I'd download a tool called
Process Explorer from Sysinternals (freeware) and see where the CPU usage is going. It can even show you what THREAD inside of a process is using CPU time, and unlike Task Manager, device driver deferred procedure calls are reported accurately rather than listed as "idle cpu time". That helps spot broken device drivers.
Basically, run Process Explorer and then re-run the app that is so slow in the background. See if you notice anything unusual and report back.
Good luck.