Two things. First, from your bug report, when you run Cytoscape from the command line, you definitely seem to be using a Java 8 JRE (class file version 52 is Java 1.8). Making sure that you have an installed Java 11 that is on the path will help us resolve this. Second, can you generate the same errors you’re seeing and then find the “framework-cytoscape.log” file in $HOME\CytoscapeConfiguration\3\. That may have the stacktraces we need to find the exception you are seeing. By the way, have you installed any new Cytoscape apps recently?
– scooter