Perhaps the "seed time" setting under queue/seed can help. That could be the time that Deluge spends trying to seed before rotating through the queue.

I have heard of this issue, though it has only happened twice to me (out of 300+ torrents).

Have you enabled "automatic management" (or whatever) for each of your torrents? I believe it is enabled by default. I have been having similar issues cycling both uploading/downloading torrents but thought it was because I had explicitly disabled automatic management for a certain number ...