Thanks John. Good to hear you're finding CodeRunner useful.
If the question that gave you problems with the latest version on Git was one for which you had written your own template, then it's possible you ran into the bug I alluded to earlier, where a particular sequence of actions in creating a question led to a combinator template running once on each test or a per-test template running as a combinator. As I recall, it was fixable just by re-editing the question and setting the correct value in the is-combinator checkbox.
I just re-loaded the December version into a Docker Moodle image and it seems to be doing all the basics OK. If you run into the problem again, would you mind posting a detailed description of what you did to create the problem, plus a screen shot, please?