Here is a link to a FAQ on name checking:
http://www.fbi.gov/page2/nationalnamecheck.htm
I can't remember where I saw that at some point in the nineties the records changed to electronic format, and before that were paper based. I believe the paper based is very slow.
The relevant quote from the FAQ follows:
"A secondary manual name search conducted within 30-60 days usually identifies additional requests as having a "No Record." The remaining name checks (usually about 10% of the name checks originally submitted) are identified as possibly being the subject of an FBI record. At that point, the FBI record must be retrieved and reviewed. If the record is available in the FBI's electronic record keeping system, it can be reviewed quickly. If not, the relevant information must be retrieved from an existing paper record. Review of this information determines whether the information is positively identified with the name check request. If the information is not identified with the request, the request is closed as a "No Record," and the requesting agency is notified as such."
You might have hit the paper record slowdown
And now, more information from an older document, I think this is the document from where the nineties thing came from, it mentions 1995 as the date when the electronic records system was introduced:
http://www.fbi.gov/congress/congress03/garrity071003.htm
"I have touched upon our IT systems shortcomings, but now I want to discuss the primary factor in any delay in the FBI responding to a visa name check. When the NNCP systems produces a "Hit" or an "Ident" that requires further review, the analyst must consult the actual file. If he or she is lucky, the file has been uploaded into our electronic recordkeeping system, ACS, and can be instantly accessed from her workstation computer. This system only came on-line in October 1995, so often the full text of the information has not been uploaded and the analyst must resort to the paper record. Paper records are divided into two basic file categories: active files and closed files. Active files are, as the name suggests, current, on-going investigations, analytical projects, or administrative functions. Closed files are records of past investigations or functions, now inactive, but for which the FBI is required to retain the records, either in satisfaction of statutory authority or regulations, or because the information contained in the closed file represents a key component to FBI's intelligence base.
FBI files are currently stored at one of approximately 265 locations, including the FBI's Headquarters facility, several warehouses around the Washington Metropolitan area, in records centers either operated by the NARA or commercial concerns, four large Information Technology Center facilities on the east and west coast, at each of the 56 field offices, many of the larger of our 400 resident agencies, and at legal attaché offices worldwide. This equates to approximately 1.8 million cubic feet of decentralized records storage, which provides some unique challenges to our efforts to be optimally effective and efficient. While the FBI's decentralized paper records management process does ease field investigations and local prosecutions - a process that may have sufficed before September 11, 2001 - those terrorist attacks have forced the FBI to shift from parochial investigations to nationwide intelligence gathering and sharing.
In addition, statutory authorities for domestic law-enforcement and international intelligence agencies have been expanded (e.g., USA PATRIOT Act), increasing the number of agencies requesting FBI information. As the FBI is called upon to share and/or jointly investigate complex cases, it must share information internally and with other cooperating organizations. Currently, analysts conducting research on terrorism or intelligence topics who develop leads based on information indexed in files located outside Washington, DC must request those files be retrieved from the shelves and shipped to FBI Headquarters. The decentralized records management system hinders timely nationwide investigations and information sharing, since much time and effort is expended simply locating and shipping files across the United States. Beyond file retrieval delays, records security and document safety are also a growing concern.
Delays have resulted from NNCP personnel identifying a file's location then requesting the file from a field office. Time delays mount as field office staff search file rooms and then ship the needed file or a prepared summary to FBI Headquarters. This process – repeated for many tasks, not only dilutes the FBI's responsiveness, but also limits information sharing – a critical success factor in working counterintelligence and counterterrorism cases. The name check delays have significant consequences to FBI customers and stakeholders. The delays impede hiring or clearing skilled workers; completing government contracts; student enrollment, and as is the interest of this Committee, clearing requested visas for business visits to the United States. More importantly than all of the foregoing, these processing delays can also diminish counterterrorism effectiveness.
One possible solution to these problems the FBI is exploring would be a central records repository where all of our closed paper files could be located, and our active files stored electronically. Our frequently requested closed files could be scanned and uploaded into our electronic record-keeping system, so that Agents and analysts world wide would have instant, electronic access to the information they need to do their jobs.
Conclusion
All of these efforts reflect the FBI's recognition of the importance of accurate and timely name check processing. I want to emphasize to you, this issue has the full attention of Director Mueller. The FBI appreciates the interest of the Committee in this matter. I thank you for your invitation to speak to you today and look forward to working with you in the future. I am prepared to answer any questions the Committee may have."
PS: I hope people start referring to this thread, because it is becoming a bit tiresome to answer the same name check questions again and again, by me and others