One data point … I just tried it … no problems installing from App Manager. All apps downloaded and installed … restarting Cytoscape also had no problems.
A drastic experiment would be to rename your CytoscapeConfiguration directory (in your Windows user directory) to something else, and then restart Cytoscape and do the install again. Does the situation recur??
Could you be behind a proxy that could have a bad copy of a JAR??
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