The possible theory: When VCM (ECO mode) is enabled, it disconnects the valves from some of the cylinders, then at the same time the fuel injectors are not opened by the solenoids (simply the ECU doesn't send the signal to open every inlet cycle) and the cylinders are basically disabled that way. However, the fuel pump is still providing pressure and if the fuel injector doesn't close of completely, it will slowly leak and fill up the cylinder, thereby wetting the spark plug. Every time the cylinder is afterwards enabled again, there is a very rich mixture, which will cause soot deposits to build up on the spark plug. After a couple of cycles this way, the spark plug will be so sooted and wet that it will simply not spark properly anymore.. which leads to the misfire..
A good bet is that disabling the VCM system with a muzzler, will prevent the slow drip from the injector being problematic as each ignition cycle the small amount of extra fuel will simple burn up. It's probably a negligible amount if the cylinder is in constant use. It may still leak a little when parking the car, making it sometimes a little harder to start after parking for longer than a short time (enough fuel leaked to be noticeable) , or shorter than a long time (fuel pressure dissipated, and fuel has evaporated).
Recommendation: Install the VCM muzzler. (I did it with a simple 100Ohm resistor type muzzler), but more intricate versions exist that prevent false engine temp readings during overheat conditions. Suggest you read up on their functioning and make a decision on which will suffice for your use and level of comfort.