The System Restore process introduced in Windows Vista regularly creates backups of your data using a feature called Volume Shadow Service (VSS). This feature does a lot of work in the background to make sure that you never lose any data. Unfortunately, during defragmentation, it can try a little too hard and create extra backups that you just don't need.
So, if you find that you have lost free space after defragging (and this goes for all defrag tools, not just Defraggler), VSS is probably the cause.
Luckily, Defraggler allows you to disable VSS during defrag.