You need to find a way to reproduce the issue. If it happens with regular pictures, it's tricky to diagnose, because it may require lots of shutter actuations to find a pattern. If it happens with silent pictures, it should be easier (e.g. leave the camera overnight on an external power source, taking pictures).
To rule out problems caused by other software or devices, format the card in the camera (and restore ML) before each shooting session.
Once you can reproduce the issue, you can narrow down by changing settings (e.g. turning off what you don't use, resetting ML to defaults, unloading modules).