That is quite odd. I can't say I've ever experienced a bug like that, nor do I know what's causing it, but it does seem plausible that something in the file is corrupted. I recently had a file become corrupted and this strategy helped me restore the project. It may not solve the issue, but it isn't too difficult to do and never hurts to try.
Create a new empty project, open the browser icon (in the top right, the icon with a piece of film reel, a camera and a pair of eighth notes). Select the third option "All Files" and then search for your Logic project by name. Highlight it by clicking once, and in the bottom right the option to "Import" will appear. This will create a menu listing all of your instruments, auxiliary sends, master settings such as tempo, etc. Make sure all 6 of the options above the menu are selected: Global, Audio, Inst, Aux, I/O, MIDI. The goal of this exercise is for Logic to rebuild an exact copy of your project hopefully without any corruption or glitches as seen in the original.
Go ahead and select every track, and tick every available box (Content, Plugins, Sends, etc. all of them). Once you do this click "Add" in the lower right corner. It will ask you if you want to replace or add auxiliary sends, since this is an empty project I believe adding will do just fine. Hopefully this will rebuild your project 100% correctly, but remember if it doesn't, it WILL NOT affect the original project so go ahead and delete if you would like to.
Also please note: depending on what is wrong with your project under the hood, importing may not work entirely correctly. That's ok! I recently did this and rebuilding created some sequencing and aux send issues. My way to solve this was to import the project in smaller bits and also to not allow it to import tempo information from each track, as somehow that had gotten messed up in the original project and was the cause of the sequencing issues. All that goes to say, don't stress if it doesn't rebuild exactly right, there is most likely a solution.
If you choose to try this solution and it doesn't solve the automation issues let me know, I will try and brainstorm another solution. Bouncing the busses does sound like a decent workaround although it is somewhat limiting if you are still adding to the track, plus a part of me believes you can solve the issue without a sneaky workaround.
