When running tests with run-test.sh I find that the class argument must be the last argument for the tests to run correctly.
For example,
php scripts/run-tests.sh --url http://mysite.com/ --class MyTestClass
correctly runs the MyTestClass test on the specified url.

However,
php scripts/run-tests.sh --class MyTestClass --url http://mysite.com/
results in the following error:

ERROR: No valid tests were specified.

On line 219 of run-test.sh, the following code appears to reset the test names passed to the script from all earlier arguments:
$args['test_names'] = array();