Um, wouldn't it be less confusing if it said Move Right / Move Left or Position to Right / Position to Left?
In testing this, I also realized that there isn't an Apply button. (Yes, I am using multiple titlebar buttons on the caption.)
The only way, really, to make it less confusing is to have the button arrangement show itself on the settings dialog (so you can see the layout you're setting up). Then you can hit "apply".
I'm going to leave it as up/down, as I don't think left/right is any less confusing. In that interface you really are moving the buttons up/down in the list to arrange their display priority. I think that's as much sense as I can make it. I will look into adding an Apply button for Beta 9. Thanks!