If anyone is interested, i fixed the problem.
It was a simple matter of a broken wire connection.
Since the Charge goes up when the vehicle is charging and in general works fine as well as everything else, corrupt EMS software is out of the question since if it was corrupt it would most likely not run at all and not connect to the EMS manager since you need to really try and corrupt the internal EEPROM on a PIC microcontroller (the controller which runs the EMS).
Since it only doesn’t drop then the problem was in the power (Ah) measurement while driving and in general while draining the battery. The EMS measures the battery through a simple 2 wire connection to the negative pole with a mechanical resistance in between. You shall find this if you look just after the contactor. There will be 2 thin wires connected (Red and White) with screws to the main power pole. These two wires go into the main EMS connector (CN64) and are the only 2 thin wires. The third is just the shielding and doesn’t go anywhere although connects to what i assume is the GND on the connector.
Visually both wires were connected firmly to the connector but when testing for continuity there was none. A simple way to test this would be to connect one terminal to the Red and one to the While cables. Normally there should be continuity. Turned out that the wire was held only by the rubber sleeve and there was a broken connection. Re soldered the wires and everything works fine now.
It would be pointless to check for a broken connection inside the wire since it is well protected by the metal shield and is most likely to brake at the terminals if someone is going to do this test. These are the only 2 thin wires on the connector so they are likely to brake if you pull the connector too hard when disconnecting.
I personally recommend NEVER to use crimp connections and ALWAYS solder the wires. This problem could also give false or erratic readings on the Power meter in the vehicle if the connection comes and goes so it is reasonable to check this first if you have a similar problem.
Hope this helps someone else if the same problem occurs.