A diode combiner and a Prolsocharge are similar devices and provide a similar benefit when the engine is running, albeit the diode combiner comes at a cost of 0.7 volts in voltage drop and the Prolsocharge is 0 voltage drop. Unfortunately, the Prolsocharge only works when the ignition switch is turned on. Your diode combiner worked regardless of the ignition switch; as such you could use the diode combiner with charger, solar, and alternator. From your description, it seems that your charger output was connected to the diode combiner. From the diode combiner, all three banks received a charge.
Your charging system needs to be changed. To charge all your banks with inverter/charger and solar, you'll need to use a paralleling devices, such as a Blue sea ACR.
The fact that your batteries are GEL and flooded is a very SERIOUS issue. GEL and flooded batteries need completely different charging curves. Many boaters confuse GEL and AGM; make sure your batteries are GEL. If your alternator is not externally regulated, you'll quickly kill your GEL batteries by overcharging them. Your diode combiner, with its 0.7 voltage drop, probably acted as an externally regulator, bringing the alternator output voltage to 13.7 V from 14.4 V. The Prolsocharge has 0 voltage drop, this is a problem for your GEL batteries, since the GEL batteries will receive 14.4 V.