Sorry for being so slow to reply (4 months!).

I finally got around to upgrading to 2.1.1, but it has made no difference.

I can also confirm that per-torrent upload limits work fine.

It's in the bandwidth section.

Deluge 2.0.3 (running on Ubuntu), completely ignores my upload speed limit. For instance, I currently have my upload speed limit set to 400 kiB/s, but quite often I see uploads going at 1MiB/s or faster. How can I enforce my speed limit?

Try right-clicking on the torrent in question and selecting "force recheck".