Hi Henrik.
I will recommend you to use the Real-Time Execution Trace toolkit. It enables you capture and display the timing and execution of VIs and threads for the application running on your RT target.
A trace could look like this:
In the top section you have the Thread View, that shows all the threads that are running on the system, including all the threads you are not explicitly handling, like timing and communication threads.
In the button section, you have the VI View, where you can monitor if your different VIs are executing or if some of them are causing a starvation; meaning that higher priority tasks are using too many resources, so that lower priority tasks are never executed.
Another way of having a look at the resources are the Distributed System Manager. It can basically tell the same as the "Get CPU Loads" VI you are using, however it also offers the possibility to see the running states of the VIs (Note; In order for this to work, you need to enable VI Server on your RT Target).
I hope these tools can bring you closer in determine which VI are consuming your resources.
