I was having this problem as well. Was not sure about the config, I looked through the options and could not find filemonitor anywhere. I finally went to the Tools tab and clicked on File Monitor. Then I unckecked the boxes. Seems to have worked.
to be honest, unless you have a specific reason to be using it, running file monitor all the time is not a good idea. It's a feature that slows things down and unless you are always having movies added each time it starts, it isn't needed. I actually do add movies almost every time I fire up EMM and I still do the couple of clicks to search my drive for movies....so default, don't have it on!