I would expect that these entries in your climate file are simply not
represented in the the cumulative sky model. A way to work around this
might be to hack gencumulativesky to provide gendaylit with explicit sun
positions and artificially increase the altitude to be above 6 degree.
It would be interesting to know the source of the values below 6 degrees, as typical sky scanners are not able to measure these directly. This means that the values represent probably not measured but derived data (total horizontal irradiance - diffuse horizontal irradiance).