Hi Patrick,
I'm not sure what specific server setup could cause this. At the moment, we're struggling with finding a reliable AND easy way to determine what blocks are used.
Maybe understanding the inner workings of the plugin will help you to find your solution. You can find that here: https://github.com/trendwerk/multiple-content-blocks/issues/54#issuecomment-54327005.
If you have any ideas about better ways to accomplish this, I would love to hear them. If you have more questions, feel free to ask.