When using a Multi-configuration project (from the Matrix Project Plugin) together with the Plot Plugin I've found two issues:

1. Plots are not displayed after restart. No plots are displayed until you run the project at least once after the restart.
2. When configuring the project all the options are not displayed as they should. For example clicking on the "Load data from csv file" radio button does not show the options "Include all columns", "Include columns by name" etc. instead "Uncaught TypeError: Cannot read property 'next' of undefined" is written to the javascript console. (This might require more than one plot to reproduce, not sure)