Capicators are kind of strange beasts,, If you have a large electrolytic type that is operating at say half its voltage.. (or less) it may not be working at the same capacity (Farad wise) either... But if it is designed that way, and Progressive Dynamics likes to slightly over design (Good thing in my opinion) that should not be a problem.
Factors affecting charger rate
Limiters in connverter
Converter output voltage (Measure it before you attack with screwdriver) this will tell you if the problem is internal or external
Wires between converter and batteries
All those lovely corroded connections
The internal resistance of the battery.
Battery state of charge (Resting voltage).