What's the difference? Do I have any control which is used?
Button Controller 5 introduced some new features, like the use of hub variables. Button actions are also now separated out into separate "grandchild" apps, one per button event, which makes the behavior of the various timed actions and cancelations clearer. You can read more in the 2.2.8 relese notes:
You don't have control exactly over version, but anything you create as new will be the latest version. There is no need to recreate older instances, as they will continue to function and remain editable (just not with the new/different features).