David -
I've been researching a one-company "scout" unit for many years, even ordering all the military records from the archives, so I know precisely who was in it. Imagine my surprize when the NPS's Soldier Sailor System (S-S-S) did NOT list several of them. The reason (in my case) is that the data consisted of xeroxed pages of soldier index records, input into the S-S-S by volunteers. Obviously, one page of the soldier records was lost and thus didn't get put in. Tho I notified NPS about the mistake and provided the missing men's names, I don't know whether a correction ever was made. (maybe I'll check?)
Perhaps the ancestor of individual you are trying to help also was accidently left off the S-S-S ? The S-S-S is a secondary, quick-'n-dirty first place to check only, and not for in-depth research.
John