I've just seen exactly this behaviour (takes many minutes to progess from "[info] Writing changes to Deluge config file '/config/core.conf'...", WebUI nonresponsive, and deluge-web pinning one cpu core at 100%), and have found what was causing it for me.
'\appdata\binhex-delugevpn\web.conf' had grown to over 40MB causing both the config-parser script and deluge-web to choke trying to parse it. Looking at the file this was because there were thousands of 'session' entries; I'm guessing that it caches active sessions to the webui in the web.conf, but for some reason never clears them, causing the file to grow out of control.
Stopping the image, deleting all of these entries (bringing the file down to a much more reasonable 620bytes), and restarting the image made everything start up quickly with the webui working as normal.
Hopefully that's helpful to someone!