Bush and Congress appointed an Inspector General to oversee the issues with federal agencies like NASA wasting money. That's why. If one reads the links they will see letters to Congressmen justifying their activities. Do you think they write letters to Congress every year as standard procedure? There was a lot of heat during those years. When Obama came in, in 2009, he wasn't interested in heavy oversight of Federal agencies. The GAO doesn't do such violating audits every year.
Per decades prior, there isn't really that much online from the 60's, 70's and 80's. But consider: Companies and government agencies usually only improve their financial management. In 2005 if they were totally unauditable, what makes you think that 1985 NASA was a saint? Why would they downgrade a good process of financial management? "Nah, we don't need to keep good records or perform internal financial audits anymore. Lets stop doing that. Boring." Are we to assume that this is what happened?
Then why was it not revealed NASA had been mismanaging finances since it's inception? That's a pretty big revelation. Surely they didn't just stop at 2002 and say "eh 2001 is probably fine we don't need to keep going back." Especially during this sensitive time period as you said.