The S99local link is not present in run level 4. I reckon that in the mysts of history, run level 4 was supposed to be run level 3 with network support. In initscripts rc3.d and rc4.d are identical, except that S99local is missnig from rc4.d. So, as the result, run level 4 does not update /etc/issue, etc...
will be fixed in the first release *after* 5.99-1.