I used to have a Convoy S2+ with XML2 and 7135x6 so 2.1A max and 850mA in medium mode that I used most of the time on my bike. I used Panasonic 2900mAH 18650 cells with those and my VC2 charger has always been fine with those. That light got damaged so I bought a Convoy S21 with Nichia 519. I used the Panasonic cells but found the battery life suboptimal because I would only get about 80 minutes run time in the 1.35A medium mode.
I bought a few Samsung 50E 5AH cells from from Battery Junction. A few times I found that after 4-5 hours that the charger is pointing to 100mAH and I only have 600mAH added so I don’t understand what is happening.
try vapcell S4 plus please， 
The VC2 only charges up to 500ma if I remember correctly. You are going to need at least a 1amp input into the charger. I don’t know what kind of supply you have your cord plugged into but read the label on it and see what it’s output is, then divide that in half because most of them lie. 
Yes - it is supposed to be capable to charge 500mA per channel x 2 channels.
Anyways the USB power supply is probably the culprit here. I was using an old Blackberry 850mA USB power supply. I don’t have two batteries depleted to test right now.
I hope that will solve your issue. I have a few of them. They work really well. Really slow but, really well. 
Look at the screen on your VC2 charger. Does it indicate full current, or did the current dial step down?
I use a VC4 and the current dial used to step down all the time. After getting a new phone (with a higher current charger), and replacing my previous USB brick with the new phone charger, the problem went away completely. So chances are that the USB charger is the problem.
It turns out to be the micro-USB cable. The charger would start out at 500mA but step down to 100mA some time later even with the new 1A power supply. It did not matter if 1 or 2 batteries were in the charger.
I changed to a new cable and it seems to charge 2 batteries at 500mA without issue last night. But sample size is 1 right now.
Wish I could have DC barrel connectors again…I have a 2 slot Xtar charger somewhere with 12V 1A input and a 5.5 x 2.1mm barrel jack. The slide rail rusted so much that it would not get a good connection and would not detect the battery. Then the plastic bits inside broke when I disassembled it to remove the rust. I’ve covered my VC2 with grease and it does not show any rust after 5 years. Or maybe they used different steel. No idea.