But in uTorrent, it is a bit complicated to force the data integrity check. This will be required to resume your download from linux or windows. I use Deluge in that case. And before I start the download, I just do right click and check Data integrity, so that it can count the additional data I have downloaded from Linux or Windows.
And it is available natively on both Windows and Linux. It also has the scheduler thing for night time unlimited connections.