I've not followed the IRS scandal in detail, mostly because as a liberal I doubt if there's anything much there. The latest is IRS is unable to provide Ms. Lerner's emails from a period in 2011. The right is screaming 18 1/2 minutes, the left is blase.
Megan McArdle says the IRS story is possible.
I've no idea what actually happened. When I came to ASCS, the records management people were still remembering the Billie Sol Estes scandal (a Texas wheeler-dealer, one of whose scams was transferring cotton acreage allotments from one county to another in order to make more money). Congress tried to investigate, and found the ASCS correspondence and records were in a mess, resulting in establishing a new system of central files and documentation. They were proud of the system; I remember in the 70's they showed it off to a visiting Soviet representative(s). The system worked with the hierarchical nature of the organization: correspondence came up the line or from the public, replies went down the line or to the public, decisions were made using CCC board dockets mostly, or reflected in memos or directives to the field.
By the 90's, everyone who'd been involved in creating the system was gone and there was no one left who really understood the importance of records management. And since the early 80's we'd been using one email system or another (Wang, Dec Allinone, etc.) finally ending with a central email system. Telecommunications costs had come down and we used more conference calls etc. But the multiplication of communication channels and the gradual decline in the hierarchical nature of the organization meant there was less of a clear division between decisions which were considered official records and those which were not. And when you looked at email that was especially true. The initial starting point was that not all emails were official records, those that were had to be printed out and stored on paper in established files.
Bottomline, by the time I left, I had no confidence in the record management of FSA--management had never given it the time and money it required. Another scandal might lead to a change in the situation, but it was very unlikely to be solved otherwise.
I don't know whether the same situation held in other government agencies then, or in IRS today, but I wouldn't be surprised. Here's a link to a search on the GAO site for records management.