1. The "thunk" sound is used by the Extended Player window when targeting specific categories of targets. Open the Window Manager to the Player/Extended Player page and uncheck all the checkboxes in the area shown below. Does that help?
2. DarqUI doesn't have an effect on whether you receive credit for quests, but you can disable it and run through Golden Rule again. Type /loadui and choose Default from the window that appears, which will disable DarqUI entirely. When you are done you can go back and choose DarqUI Unified from the same window to re-enable DarqUI. You should not need to reinstall anything.
