Hey,
Just to be on the same page, try setting up CC using bizhawk 2.6.1. We officially support his version now and have been doing most of our tests with it: https://github.com/TASVideos/BizHawk/releases/tag/2.6.1
Once you have a game launched through the CC desktop app, you want to try testing effects before going live. OOTR just required you to be outside of Links house for effects to activate. The “Live Extension” button and under Game Controls “Effect List” will let you test effects. Try effects using this method and let us know if it still doesn’t work. Launching the desktop app as admin may be worth trying as well.
Also worth noting, if you have Spectrum as your ISP, there may be connection issues with CC and we have some work arounds at Do you have Spectrum?