Successfully executed 10000 generated tests for 10000 generated classes 
(generator in attachment) with EclEmma on Windows 10, Mac OS X and Linux.

As wild guess: connection between JVM with tests and IDE is established at 
startup, data is written at termination (shutdown hook). Is it possible 
that something in your environment (OS, firewall) kills connection while it 
is inactive between opening and writing? How long execution of tests takes?

Regards,
Evgeny

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import os

os.makedirs("src/main/java/")
os.makedirs("src/test/java/")

file = open("pom.xml", "w")
file.write(
"""<?xml version="1.0" encoding="UTF-8"?>
<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";>
  <modelVersion>4.0.0</modelVersion>

  <groupId>org.example</groupId>
  <artifactId>example</artifactId>
  <version>1.0-SNAPSHOT</version>

  <properties>
    <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
  </properties>

  <dependencies>
    <dependency>
      <groupId>junit</groupId>
      <artifactId>junit</artifactId>
      <version>4.12</version>
    </dependency>
  </dependencies>

</project>""")
file.close()

for x in range(0, 10000):
    file = open("src/main/java/C%d.java" % x, "w")
    file.write(
"""
public class C%d {
}
""" % x)
    file.close()

    file = open("src/test/java/C%dTest.java" % x, "w")
    file.write(
"""
public class C%dTest {
  @org.junit.Test
  public void test() {
    new C%d();
  }
}
""" % (x, x))
    file.close()

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