I had a similar problem with my 1996 sl320 although your specific model may differ.
Remote would not work until I unlocked the car from the inside central locking switch. The This also de-activated the immobilizer.
As an alternative there is a separate key on the siren in the engine compartment which also de-activates the immobilizer.
The infrared remote keys are prone to stop working if dropped and replacement is expensive and need to be ordered from Germany.