There appears to be a small bug in the syskeygen Bash script for 5.0-alpha5 which causes the key file name to be incorrect. Here's the patch:
diff -u bin/x-pack/syskeygen.orig bin/x-pack/syskeygen
--- bin/x-pack/syskeygen.orig 2016-09-09 23:19:15.845900029 -0700
+++ bin/x-pack/syskeygen 2016-09-09 23:00:49.717433221 -0700
@@ -94,7 +94,7 @@
fi
cd "$ES_HOME" > /dev/null
-"$JAVA" $ES_JAVA_OPTS -Des.path.home="$ES_HOME" -cp "$ES_CLASSPATH" org.elasticsearch.xpack.security.crypto.tool.SystemKeyTool $properties "{args[@]}"
+"$JAVA" $ES_JAVA_OPTS -Des.path.home="$ES_HOME" -cp "$ES_CLASSPATH" org.elasticsearch.xpack.security.crypto.tool.SystemKeyTool $properties "${args[@]}"
status=$?
cd - > /dev/null
exit $status