Rush
The LED is not really required, and after blowing out 2 on my prototype charger, I am going to use a slightly different system. A standard led any color, and a parallel resistor. The resistor will pass most of the 350ma to the batteries, and the led will light up showing that current is flowing. I just need to play with the resistor values to determine the best combo.
MrMik
The LM324 like all op amps can operate as a comparator, but you should also look into true comparator chips like this one.
LM311 - Voltage Comparator
they have more flexible input and output setups, and many have special internal hysteresis circuits, and usually have an open collector transistor output so they can safely drive a relay or higher voltage device than the power supply for the comparator inputs.
You must have noticed that as you increase the hysteresis the difference between the set-point and the actual turn off point got bigger. this makes it difficult to simply set a value and have the turnoff happen at that value, but if you adjust the setpoint dynamically what you have will work fine. 500K is still a reasonable number, but the real issue is that you must have a lot of HF noise in your setup.
A look at your schematic shows why you are still having issues.
1. The capacitor across the setpoint pots should be cap - to negative 6V, cap + to pot wiper
2. The cap across the PTC strip wants to be cap- to negative 6v, cap + to junction of r5 and r4.
3. The lm324 is rated for 25ma output current. pin14 is driving an led and a relay, and may be exceeding its max current which will make the circuit unstable. I much better way to drive the relay is to drive it with a transistor that the op amp turns on, so the relay current is handled by the transistor.
adding more hysteresis of course will let it switch cleanly even with the noise, so if it is doing the job leave it as is.
The accuracy of switching will be effected by the actual 6v power supply voltage, so for a more accurate system, one must regulate the voltage feeding both the PTC strip voltage divider and the setpoint pots.
keep playing you will understand it all eventually.