I think it is just an extension of this bug. After it happens, you can no longer activate/deactivate the first step in the second chained track. If you push step 1 in the second track, it activates the first step in the first track. I usually clear a track by toggling steps individually (when working on a specific sequence)
I tried actually clearing the track (with CLR mutator) and it did eliminate the bad step. So I guess it is not permanently damaged.
You said it would take some considerable work to fix this bug though right? 
Thanks!