testNewView_colourThresholds passes in Eclipse (mostly) put not when run from CLI

testNewView_colourThresholds fails when run via the CLI as part of the test suite i.e. via 'ant testng'. Output:

[testng] FAILED: testNewView_colourThresholds
   [testng] java.lang.AssertionError: expected [true] but found [false]
   [testng] at org.testng.Assert.fail(Assert.java:94)
   [testng] at org.testng.Assert.failNotEquals(Assert.java:496)
   [testng] at org.testng.Assert.assertTrue(Assert.java:42)
   [testng] at org.testng.Assert.assertTrue(Assert.java:52)
   [testng] at jalview.gui.AlignFrameTest.testNewView_colourThresholds(AlignFrameTest.java:546)
   [testng] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
   [testng] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
   [testng] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
   [testng] at java.lang.reflect.Method.invoke(Method.java:498)
   [testng] at org.testng.internal.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:85)
   [testng] at org.testng.internal.Invoker.invokeMethod(Invoker.java:648)
   [testng] at org.testng.internal.Invoker.invokeTestMethod(Invoker.java:834)
   [testng] at org.testng.internal.Invoker.invokeTestMethods(Invoker.java:1142)
   [testng] at org.testng.internal.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:124)
   [testng] at org.testng.internal.TestMethodWorker.run(TestMethodWorker.java:108)
   [testng] at org.testng.TestRunner.privateRun(TestRunner.java:771)
   [testng] at org.testng.TestRunner.run(TestRunner.java:621)
   [testng] at org.testng.SuiteRunner.runTest(SuiteRunner.java:357)
   [testng] at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:352)
   [testng] at org.testng.SuiteRunner.privateRun(SuiteRunner.java:310)
   [testng] at org.testng.SuiteRunner.run(SuiteRunner.java:259)
   [testng] at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
   [testng] at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:86)
   [testng] at org.testng.TestNG.runSuitesSequentially(TestNG.java:1176)
   [testng] at org.testng.TestNG.runSuitesLocally(TestNG.java:1101)
   [testng] at org.testng.TestNG.run(TestNG.java:1009)
   [testng] at org.testng.TestNG.privateMain(TestNG.java:1316)
   [testng] at org.testng.TestNG.main(TestNG.java:1285)

When run in Eclipse, as part of the test suite, testNewView_colourThresholds passed. When I ran testNewView_colourThresholds as a single test it failed the first time. When I ran the full set of tests in the class, testNewView_colourThresholds passed. Further attempts to run testNewView_colourThresholds as a single test all passed.

Edit: it appears that running the full test suite then running testNewView_colourThresholds individually in Eclipse reproduces the test failure.