I only use the mh-32 charger, non compatible batteries fail to charge by the 2nd charge on,"so after the camera understands its not an original nikon battery".
Let me have this straight: 
You only use the original 
MH-32 charger
Non-original batteries 
fail to charge.
BIG Question: by what means do you realize that battery has failed to charge? (quickly 
flashing LED in the MH-32, or 
a message from the Zfc ?) 
On the MH-32 you have three possibilities:
1) If the battery is in the process of charging you have a 
slowly blinking LED light (one every 2 seconds approximately)
2) If the charging cycle ended OK, you would have a 
steady LED light (but then the camera must have a sort of 
watchdog to dump non-originals, maybe some parameters were not updated in the battery? Usually the number of actuations is 
reset to ZERO when battery is recharged)
3) If there is a 
battery error  you have a 
quickly blinking LED light (4 times a second) and battery does not charge. Usually this happens when a battery is 
defective (for example, if battery has a severe 
undervoltage, say 2.5V. Good voltage is between 
7V and 
8.1V). Any voltage tester wil tell you the actual voltage at battery terminals to confirm or negate that. You need very thin contacts on your tester.
The other problem (battery discharging when not in use): Do you 
turn off your camera when not in use? Do you have 
Airplane Mode Off? To save battery you should have Airplane Mode ON (means ALL wireless connectivity -bluetooth, wifi, ...-  TURNED OFF), and then turn Airplane Mode OFF only when you want to use the remote, or you want to connect to a wi-fi network 
Another question: what is the brand that's giving you problems?
Ciao from Massimo