just a thought to try.
With a new sequence if you change the one channel down, and then can you use the copy and paste with one effect on that line, does it bring the CHANNEL intensity with it, or only the sequence data?
e.g. put one off a cell or two out, then click the channel header to select the entire line, copy it, and then go paste it into another channel and see if the intensity you lowered came into that channel as well or only the sequence itself.
obviously won't help much with an existing sequence, but could be nice for anything you do going forward if it works.
Alan