Alrighty, I think I found the problem. When I created a new instrument (Inst 9 in this case), Logic was assigning it to an instrument track I had deleted long ago, which is also Inst 9, except not all the Inst 9 channels were deleted in the Environment. When I found those left over channels and deleted those also the automation issue worked normal again.
The more concerning issue with all this is Logic kept crashing when I tried to add any new instrument tracks after creating the Inst 9 track (when it was still linked).
How do I make sure this doesn't happen again in the future? If I delete a track that has multi channels/tracks in the Main Window but I miss one of the channels, how do I make sure to find all the remaining channels? Is the only way by browsing the Mixer page in the Environment?
Thank you.