On 1 Jul 2016, at 3:31, じょいすじょん wrote:
Saving via command s no longer works in the bundle editor window. Saving does work via the File menu.
Since the menu item works, it would indicate that something has “stolen” ⌘S.
In the bundle editor, try Bundles → Select Bundle Item… (⌃⌘T).
Then switch to Key Equivalent via the gear menu (⌘2).
Now press ⌘S and see if it is registered in this window, and if so, what action it resolves to.