yes the do, deep cell batteries actually use some of the medium the diodes are suspended in everytime the battery is discharged. So you can never actually fully recharge a deep cell battery, its states it on the optima website.
With the alternator it does not use as much of the medium since there is a trickle charge to the battery while you car is running off the alternator, vs a drain on the battery that will just kill the medium. I did this with two red tops. Just take it back and get a free replacement, dont even bother trying to recharge it.