Sounds to me like your charger is working just fine on the deep cycle battery. It's probably going to take more time to reach full charge than you're used to but I think if you're patient, it will get the job done.

I'm not an expert on deep cycle (RV) batteries but I think the problem with using one in a vehicle would be the lack of CCA or cold cranking amps. An RV battery is designed for steady and slow discharge.