In looking at our internal ticketing system, we can see that you have logged this issue with us in the past. Please update to version 3.5.2 and let us know if you are still having the issue. You can simply create a follow-up to your original ticket to let us know. We can then gather some information and log the issue with our development team. There are a lot of moving parts in this problem, and it would be helpful to get a .song file from you that illustrates the problem. You can just attach your .song file to the follow-up ticket. Thanks for all of your patience.
As we understand this issue, when you add more plug-ins to your song, you are somehow recording MIDI sustain messages to an already recorded sustain lane that is in another track. This shouldn't be possible if the original instrument track is not armed. Make sure that the record enabled button is NOT selected after recording your sustain pedal. Another possible workaround would be to go into the Inspector window for the track that you recorded the sustain into and change the input to none. If you are still picking up MIDI sustain messages on the original track after doing that, then we may need to get more information and log the issue with our development team.