Ah, at some point you made a change to the PHP syntax, saving a local copy. Once you have a local version of the syntax you won't get any updates to the syntax.
it would be nice if there was a way to make minor edits but still inherit improvements automatically. can you overrride just one file/ setting in the bundle?
That's what happens, only the changed items in a Bundle are saved to ~/Library, the other items will keep seeing any changes. However the syntax is one 'item' so a change to it blocks out updates to the syntax.