Make sure you choose a 'Effect' preset (like 'Default 2 Layer') for the M/E and the positing controls will appear. It sounds like the M/E is currently configured in 'Mix' mode (a transition) which will not expose the positioner controls.
By default, each time you enter a new session, the M/Es are in Mix mode and note effect. To switch to effect mode you just have to load a default config instead of the transition icon. You chose either 2, 3 or 4 layers effects and boom, your M/E has switch into effect mode