Kenny,
I've been using a CTEK conditioner for more than 9-years on my Cayman without problems, albeit not continuously like you. Terry was referring to a trickle charger rather than a battery conditioner like your unit which should have been safe to use for an extended period. Indeed, I believe that such devices are commonly used in vehicle storage facilities, so there shouldn't be a problem using one.
Maybe the conditioner malfunctioned and allowed the battery to discharge completely? You don't mention the age of your car and if the connection was directly to the battery or via a cigarette/power socket. Direct connection to the battery is probably more reliable for long-term operation, especially if a fault develops unnoticed with the socket during the storage period.
As Terry says, the symptoms you describe are typical of low battery voltage.
Jeff