Otter:
Have you tried to initialize your mixer settings? When I have many changes to my routings and or effects and I get lost to the point of I don't know what I have done. I just re-set my mixer settings. You go to you systems icon. Then scoll over 1 screen. There should be an icon for "initialize mixer." This is either under the systems settings or the Utility settings. I don't have my machine next to me. But if you get lost, e-mail me and I will be happy to tell you exactly where it is once i get home.
The reason for your problem may be a cause of effects also. Are you using any effects? Do you have them set to pre or post? If it is on pre and then you turn down that channel, you will still hear the effect.