The ASC that took your fingerprints is affiliated with the FBI. So the prints are already with the FBI. Search results for fingerprints using the electronic scanner are returned in a couple of days at the most. I am not sure what you mean by manual fingerprints, but if what you mean is that they are not machine scanned, the fingerprints would have to be first scanned into their system. I would imagine this would add to the turn-around time but I would guess the results should be available to the INS within a week on the outside.
The other security check that takes place is a name check and this can take some time if there is a hit, i.e., a match, even if partial. I believe name checks are the responsibility of INS. I am not sure if the FBI gets involved in cases where there are matches or not.
Search for posts by users 'yager' and 'guju' for more information.