So, it might be causing by the cache, if you don't safe remove the pen-drive, it don't flush the data into the hard disk, and cause the cache loss?
And I think the cache problem will increase in windows 8(If you tick"turn off windows write-cache buffer flushing"), as I extract the Rar file, it write into the cache first with 1xxMb/s in a short time(sometimes), and the modified file showed in task manager will increase until windows think it is danger to keep too much of it and start flushing into hard disk.
But it is ok for me, as I can start running the software without waiting it flushing all into hard disk.