This periodic slowing down and speeding up is caused by setting the upload speed limit too low.
For example, if your upload speed is 3,000 KB/s and upload is limited to 40 KB/s, you will see this behavior. Try increasing the upload limit in your Bittorrent client such as Deluge, Transmission or uTorrent such that it is at least 1/20th of your download speed (3,000/20 = 150, so the upload limit should be at least 150 KB/s).
Hope this helps! If so, leave a thank you comment!