We have changed the default CPU throttle settings from 100% to about 60% to be less obtrusive to certain kinds of PC's and novice users who may own them. You can read about the details here.
The method for adjusting the throttle has been simplified via the use of a new tool which you can find from the above link.

For the newly launched HPF2 project in particular, the research code will still have occasional several minute periods during which it does not follow the throttle settings. We will be making further changes at some later time to improve this.