If the batteries are that low then they are pretty much dead. Sony VTC anything is the #1 battery that is faked. I own 2 Wismec RX200 (white/teal & black/black) and a Wismec DNA 200 "I wanted the get the whole family LOL!!" No issues with the Samsung INR18650-25R 2500mah batteries. Where did you purchase the batteries? If on eBay the chance that they are fake is about 95%. If it was a local shop that chance is about 50% that they are fake. On that mod I would use either a 2500mAh or 3000mAh batteries. Forget VTC3 its only 1600mAh, VTC4 is only 2100mAh and the VTC5 is 2600mAh, but again over priced and highly counterfeited!!
Now what version of software do you have on your RX200? The current version as of today is 1.08 which corrected font issue, but 1.07 did address performance issues. I have heard of a few users that did have a similar issue as you did. To check the version of the mod. Power off "press fire button 5 times", now press the fire button 20 times. It will display the version number. BTW if you press the fire button 10 times it display the mod's temperature. To exit press the fire button once.
The Nitecore charger that you are using is a good charger. I have the D4 version "LCD Display"