Hiya
I'm not sure exactly how you have GoCD set up, but I don't think GoCD has any way to be aware of custom git server-side policy constructs such as "blocking merges", merge policy or "protected branches". So I don't think it is possible for GoCD to behave differently based on whatever policy GitHub is enforcing unless perhaps you are relying on
webhook integration to trigger builds on GoCD, and GitHub is not making these webhook calls in these cases.
If new commits are added to a branch, and GoCD is polling those branches it should trigger a build within ~ a minute assuming you don't have contention due to too many materials, or Github rate limits etc.
If there is no other explanation in the above, it sounds like you might need to do some deeper investigation to see what is going on. If you manually trigger the pipeline, does the new commit get found? Do you see the new commits in the Materials view? What if you manually refresh the material here? What's the configuration of the pipeline in question?
-Chad