From what I understand, he was. How else did the guy in Boston back in 1999 figure out that his methodology was BS because there were not enough options sold to cover his backside on the number of stocks he (allegedly) bought. He MUST have filed paper...the books, as they say, were cooked.
However, this past president of NASDAQ and pillar of the financial and NYC community was thought to be beyond reproach so when the SEC looked at the cooked books in what must have been a cursory manner, everything seemed fine.
I believe the analysis was done against an offer from one of Madoff's conies at the time.
When everything is over and done I think we will see a remarkably sparse papertrail, and certainly no audit trail at all.