From the manual entry on the debugger:
"The estimated CPU time (e.g. 20% CPU): an estimate of how much CPU time is being spent in the logic of the game. This is not always accurate, especially since it only takes in to account time spent on the main javascript thread, and should only be considered a ballpark figure. The profiler can break this down in to how much time is being spent in each area of the game, and is described in more detail later on in this guide. This value corresponds to the CPUUtilisation system expression."
Emphasis mine.
In addition, although it's likely to provide a more accurate picture of overall system resource usage the Windows task manager also doesn't provide entirely accurate results -- it's a simple tool intended to provide a picture of computer performance suitable for general end-users -- not a precise tool intended for developer usage.