You may need to look at allowing null value values (default) and keys in the regitsry section. It will current 'drop' keys with no values. Also trying to import null value values will cause exceptions and basically trash the aip file.
Yes, we are aware of the issues with null keys/values, which also make default values completely unsupported. The main reason for that is that in MSI, nulls have different, special meanings.
A fix is underway and hopefully it will make it into the next version.