I suffered a similar CBP computer malfunction on arrival at GUM several years ago. After waiting in line for hours in sauna conditions, I was very fortunate to be skipped ahead by an airline manager (not even the one I was flying with to/from GUM) because I would have missed my connection (despite it being several hours long transit).

It seems CBP is incapable of manually processing more than a 2-3 passengers an hour per officer.