Michael,
I tried the new Beta and it worked correctly. I could assign Command-R to 'Apply Rotation to JPEGs' and the Keyboard Shortcut settings matched the menu items.
Great, thanks for trying the updated build.
One thing I noticed, but I don't know if this is by intention: When a command like 'XYZ (with prior settings)' has no shortcut assigned, it is being shown in the menu below its 'related' menu item 'XYZ'. If it has a shortcut assigned, the menu item is only shown when the modifier key is pressed.
It is a side effect of how Apple handles alternate menu items. Three things have to occur for the alternate menu item to be hidden:
1) They both have to call the same function.
2) They both have to have a keyboard shortcut assigned
3) The alternate needs to have the same keyboard shortcut as the main item and it has to have the Option key as part of its shortcut.
To fix this, Record Command-Option-R for the alternate menu item for Apply Rotation to JPEGs.
Another note: Even if you don't record that shortcut and the item remains visible in the menu, if you do hold down the Option key while choosing the Apply Rotation to JPEGs item, it will still skip the settings/confirmation. In fact, you'd have to hold down the Option key for the alternate that is always appearing in order to get it to run with prior settings. That's just how many commands in Photo Mechanic work. For more info, see:
https://docs.camerabits.com/support/solutions/articles/48001131428-the-modifier-key-Kirk
