As of Media Browser 2.2.1 (codename Firestorm) you can change the display order of your configured Media Collections in the Configurator.
On the Media Collection tab there are two buttons with an up and down icon.
Select a Media Collection and press the up or down arrow to change the display order.
Note: plugins that have their own item on the Enhanced Home Screen will always show after your own Media Collections. Right now this can not be changed.