Not sure if you use midi or not, but I have a BR1600 and use Magix Studio Deluxe to sequence drums, bass and record fader movements during mixdown. I have found that if you have a track highlighted in Magix that is tied to a different channel than the fader being moved, it will control both. So lets say there are two tracks in magix, 1 is channel 3 the other channel 4. This also corresponds to fader 3 and 4 on the BR. If I have highlighted the track in Magix that is tied to channel 3, but physically move fader 4, fader 3 moves as well. I have found that I have to be REALLY careful when I am finalizing my mix and recording the exact fader movements I want. Once i 'accidentally' record say fader 4 while having the magix channel 3 track hightlighted, fader 4 will forever be controlled by channel 3 in magix, unless I delete that midi track and start over. Not sure this is explained very well, and you made no mention of using midi, so I doubt this is your problem, but this one certainly drove me nuts for a while until I figured out why it was happening.
steve