When the main mode key is blinking green, it means your Alpha cannot find EigenD on your host computer. The keys will still light orange since the Alpha does this by itself without software running.
Check that your instrument cable is connected to the Alpha and the base station (if you have the base station pro check you've connected to the 'instrument' socket and not the 'extension' socket). Check that the base station is on, has a green light to show it connected to the Alpha, and check the USB cable is connected from the base station to your computer.
Try loading an Alpha setup from EigenD (in 1.1.14 this will be in the menu up by the clock on a mac). In later versions of EigenD there is a main EigenD window from which you can load setups by selecting them and pressing the 'load' button.
If this doesn't work, try shutting down EigenD and starting it up again, with the Alpha and base station plugged in and switched on, then load a setup again.
I would recommend downloading and installing a newer version of EigenD, 1.2.14-stable is the most recent stable version, or you can try 1.3.16-testing which is very nearly a stable release.