Do you get a message saying it's unavailable, or does the S&S just not operate?
Anyhow.. check that your S&S is not de-activated on the dashboard. If it's "off" then you will get the "Unavailable" message and the "S" logo with the line through it on the dashboard. If it's "on" then you should not see the "Unavailable" message unless something is wrong and the car has deactivated it..
You need to test the battery voltage (static and with the engine running) and hopefully tell us you're seeing 12.3v and 14,5v respectively... but test the battery directly, not via the cigarette lighter. If the battery and alternator look good (you're getting the voltages above) then the problem might be the condition sensor on the battery terminal. The quick detach post is designed so that anyone charging the battery or jump starting it, can use that (to not put the voltage through the sensor, which can kill it)... but someone might have charged/jumped the car through the sensor and burnt it.
Failing all that, are you sure the alternator is good? If the voltage is fluctuating at the battery when the engine is running then that might be a dodgy regulator. Put all the lights and the rear window de-mister on and rev the engine a bit.. if the lights get brighter, that could be a duff regulator.
Ralf S.