Did you move any data out of the hard drive, after the process? From what I've seen of my usage of the program (I am not a engineer so this is just what I observed and think is happening), the % of fragmentation is calculated by Total Size of Fragmented Files/Total USED Space. So, when I was doing the defragmentation, I moved space out of my hard drive because people said you need at least 15% of the drive free, I went from 56% fragmentation to 70%. This happens because, for example, if you have 300GB of files that are fragmented, and the total used space is 1000GB - even if your actually hard drive space might be 10 TB in total - you have 30% fragmentation. If, however, you remove 500GB from the hard drive, leaving used space as only 500GB, your hard drive will now be shown as 60% fragmented. I actually did the calculations to check this. But, again, I am not very familiar with defragmentation software so I could be wrong.
So, the percentage is now how much that particular partition is fragmented but how much of the used space is.