I'm attaching a world (whoops, is too big to attach, uhm...) Actually, the datapack is small enough to attach here, so I attached it.
Each time I reload, I get a different number of functions loaded (and indeed, some functions simply are skipped, breaking the game) - from the log:
Loaded 3554 custom command functions
Loaded 3563 custom command functions
Loaded 3557 custom command functions
Loaded 3562 custom command functions
Just do /reload a few times and watch the log.
all files loaded
some files skipped (race condition?)