I have noticed that sometime test complete script fails to execute complete scripts and log the results with Zero Warnings and Errors reason could be any but result is incomplete execution of script....
It sounds to me like a problem in the architecture of your test projects. If the code is executing and not actually "hitting" the CheckPoints, that means something prevented the checkpoint execution which, in my mind, is actually an error. I would go back through your test case and actually add conditional logical statements, try/catch/finally, etc, so that, if something should go "wrong" where the checkpoint is not executed, you'd get an error in your log.