Have you looked at this?http://wiki.linuxmce.org/index.php/Cisco/Linksys/Sipura_Analog_Telephone_Adapters
I had this happen to me, and discovered that I had a port number mismatch. In LinuxMCE admin, select Advanced -> Configuration -> Phones Setup. That brings up FreePBX. Look at the Extensions tab and write down the "Name" "Extension" "Password" and "Port" of your ATA. Then make sure this info was entered correctly into your ATA.
I bet that the main page of FreePBX looks something like the picture below. Notice that the top green bar (IP phones online) only goes halfway across the screen, when it should go all the way across. The number "1" to the right tells me that only one IP phone was working (the Media Director). When I checked the Extensions tab, it showed 2 IP phones (the Media Director and the new ATA I was trying to get working). So only 1 of my 2 IP phone was working - ergo the green bar only went halfway across the screen. My guess is that you are very close to getting things to work.
Another thing to check would be the "Telecom" dropdown from the LMCE admin page (near the top right of the main screen) and see if all settings look good.