OK, I'm probably not the best person to explain this as there are a few points that I have not been certain of myself in this area. However, some comments:
1) I have assumed (although not certain) that the per process CPU usage shown in top actually adds up to 100% x # of cores. So for a dual box, this would be 200%. The top manual page entry is a little ambiguous on this point, however I have often noticed that my sum CPU usage for the top few processes displayed in top is far more than 100%. The top manual page seems to me to imply that this is the reason why.
2) If you have a process that the bulk of the work is done by a single thread, and it is maxing out the core it happens to be on, and your box is a dual core machine, then I would expect top to show 100%, being all computing resources available for that core, and thus effective 50% of the overall machine's resources.
3) In your case, that would seem to suggest that that it is consuming 100% of one core from 4, being a quarter of the total 400% CPU available to you.... in other words 25% of the total available to the machine.....
4) The above point is highly suggestive, but not definitive - could just be a coincidence, but it is important to note that Windows definitely does not calculate CPU like this. 100% means 100%. If a CPU bound process is sucking up all CPU resources for a single thread on a single core of four, then Windows would report that as 25%. It would also look like the waveform is unnaturally "clipped" around that 25% mark rather than the more normal "spikey" look.
5) Note that Windows always has significant advantages in decompressing various video codecs as they can hand off a lot of these to the video card rather than sucking up CPU. In many cases, Linux has to do the heavy lifting directly on the CPU because of the stranglehold that M$ has on hardware manufacturers, limiting how much of the hardware we buy from them is exposed for our use!