It would be helpful to get some additional information about the error. There are two useful pieces of information we could use to solve this:
1) Any console output from running Cytoscape. To get this, run cytoscape.bat from the Windows command line. (See
https://www.computerhope.com/issues/chusedos.htm if you are unfamiliar with this) and save any output from the console.
2) The framework-cytoscape.log file (normally, it will be located in your user directory, like so: C:\Users\UserName\CytoscapeConfiguration\3)
Attach those two items to your response, and we might be able to get a better idea of when and why Cytoscape is failing.