An article by The Fort Wayne Journal Gazette points out some of the problems with background checks when conducted through government agencies. I believe most of this backlog can be cleared up by using private contractors. Not only can they get the checks done faster but when done to industry standard they are usually in most of the cases more accurate.
Fingerprint checks when done by themselves tend to only check that states database and NCIC. NCIC will only report crimes that were reported to it by each jurisdiction. You may be surprised to know that many many jurisdictions do not or can not report their information. Using a social security trace and then conducting checks on the jurisdictions that were found on the trace can reveal much more information.