Your processors aren't even close to the same.
They are from two different families. The Core 2 series was made using a larger process and slower/older memory controllers. The Core i series using onboard memory controllers, self-overclocking, is a physically smaller chip so it runs with less power (typically).
Never compare clock speeds when comparing two families of processors. You will not have equal measurements.
However, in your case, it sounds like the processor is finding it doesn't have enough to do most of the time and is slowing down (by design) and all of a sudden when your app requires it's full glory (regardless of what you are doing) it's freaking out because it's pants are off. You have to think about, as well, what this "drag and drop" operation really is. It may just look like you're moving something but there's tons (technical word) of variables involved if the app is complex.
Please clarify the following:
RAM: DDR2 or DDR3?
OS: What version?