When creating a new games database from a p/clone xml datafile, the order of selected regions will change based on the number of games per region after choosing 'ok' and then returning to the 'filters settings' menu.
For instance, if you specifiy US region as priority 1 (lets say US has 50 games in datafile) and JP as priority 2 (JP has 60 games), after choosing 'ok' and then returning back to the 'filters settings' menu (because maybe you want to verify the selections you just made) the order of selected regions will now show JP as priority 1 and US as priority 2.
Functionally there is not a problem here, original selections are effective and the database will work as intended (as long as you don't hit 'ok' again after the region order changes). But it could be confusing for someone new to the program that might think the region settings are not working properly. This behavior may be intentional, but I see no benefit if it could otherwise keep the order as selected originally.