Luke, do you have access to both the old version of logic (10.3.1) and the new version (10.5.1) ? It would be interesting to have a look at the different midi files and compare the two. If you create a simple automation with a few changes it’s possible to diff the files.
You can post it here by running xxd command in the Terminal:
xxd old_logic_working.mid
xxd new_logic_not_working.mid
copy & paste the output