Then you have to figure out what changed between when they worked and when they didn't work. We really don't have much info to go on, except that you re-installed Sonar for some reason thinking that would solve the problem. But the problem may not have been Sonar. You may think you haven't made any changes to your system, but there could have been a Windows update, a piece of spyware, an automatic graphics card update...who knows.
I don't think anyone else has experienced this issue, so it's extremely likely it's something a) involving your system, and b) not involving Sonar, because re-installing it didn't help and at one point it worked as expected. We didn't know anything about your system.
Just to humor me, could you try inserting a controller 7 value close to the beginning of the sequence on any channels that have instruments? At this point I doubt it will make a difference, but a couple minutes could at least eliminate that option.